Да, после запуска vkteams создаёт свой desktop файл в ~/.local/share/applications.
Возможно, есть способ отключить это поведение, но он неизвестен.

Ошибка не воспроизводится только на p10-server-10-x86-64.

На всех остальных системах p10 воспроизводится:
workstation-10-x86-64
education-10-x86-64
education-10-x86-64-kde
kworkstation-10-x86-64

Версии:
eepm-3.27.2-alt1
eepm-repack-3.27.2-alt1
eepm-yum-3.27.2-alt1

Исходя из кода родительского проекта
https://github.com/mail-ru-im/im-desktop/blob/78924d804fc38a5746a073d5bdb71c1c4cc97780/gui/utils/UrlUtils.cpp#L706


    void registerCustomScheme()
{
#if defined __linux__ && !defined BUILD_PKG_RPM
...
if (f.open(QIODevice::WriteOnly))


чтобы в ~/.local не создавался альтернативный desktop-файл, нужно либо запись в него запретить, либо сборку взять сделанную с флагом BUILD_PKG_RPM.

eepm-3.27.5-alt1 -> sisyphus:

 Fri Dec 16 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.5-alt1
 - distr_info: add --full-version
 - distr_info: fix Orel/orel checking for AstraLinux
 - epm repack vkteams: fix packing
 - epm play: add VK messenger
 - epm repack vkteams: prevent local .desktop creating (ALT bug 43779)
 - epm repack icq: prevent local .desktop creating (ALT bug 44250)
 - epm repack: ignore mono autoreq in generic-appimage.sh (ALT bug 43993)

На версии пакета eepm-3.28.1-alt1.noarch из билда 312100 ошибка воспроизводится.
При первом запуске ~/.local/share/applications/vkteamsdesktop.desktop всё также создаётся.
Если же удалить данный файл и переустановить vkteams, он всё ещё будет создаваться, однако, перестанет отображаться в меню приложений.

На версии eepm-3.28.7-alt1.noarch из sisyphus воспроизводится другая ошибка https://bugzilla.altlinux.org/44851

(Ответ для Vladislav Glinkin на комментарий #5)
> На версии пакета eepm-3.28.1-alt1.noarch из билда 312100 ошибка
> воспроизводится.
> При первом запуске ~/.local/share/applications/vkteamsdesktop.desktop всё
> также создаётся.
> Если же удалить данный файл и переустановить vkteams, он всё ещё будет
> создаваться, однако, перестанет отображаться в меню приложений.

У вас описан некорректный сценарий тестирования. Точнее, это вообще не сценарий. Вы проверьте правильно, упорядоченно и увидите, что ошибки нет.

(Ответ для Vitaly Lipatov на комментарий #6)
> У вас описан некорректный сценарий тестирования. Точнее, это вообще не
> сценарий. Вы проверьте правильно, упорядоченно и увидите, что ошибки нет.

Выполняя следующие шаги, ошибка воспроизводится:
> 0.1) ls /usr/share/applications | grep vkteams
> 0.2) ls /home/test/.local/share/applications | grep vkteams
> 1) # epm play vkteams
> 2) В меню приложений запустить VK Teams
> 3) Закрыть VK Teams
> 4) Открыть меню приложений
> 5.1) l /usr/share/applications | grep vkteams
> 5.2) l /home/test/.local/share/applications | grep vkteams

(Ответ для Vladislav Glinkin на комментарий #7)
> (Ответ для Vitaly Lipatov на комментарий #6)
> > У вас описан некорректный сценарий тестирования. Точнее, это вообще не
> > сценарий. Вы проверьте правильно, упорядоченно и увидите, что ошибки нет.
> 
> Выполняя следующие шаги, ошибка воспроизводится:
> > 0.1) ls /usr/share/applications | grep vkteams
> > 0.2) ls /home/test/.local/share/applications | grep vkteams
> > 1) # epm play vkteams
> > 2) В меню приложений запустить VK Teams
> > 3) Закрыть VK Teams
> > 4) Открыть меню приложений
> > 5.1) l /usr/share/applications | grep vkteams
> > 5.2) l /home/test/.local/share/applications | grep vkteams
А как вы узнаёте, что ошибка воспроизвелась? Это можно проверить только посмотрев в меню, а вы на файл смотрите.
Хотя бы нужно показать
$ ls -l ~/.local/share/applications/vkteams*

eepm-3.28.1-alt1 -> p10:

 Tue Dec 20 2022 Vitaly Lipatov <lav@altlinux.ru> 3.28.1-alt1
 - epm requires: allow show also for non installed packages, improvements
 - epm play: add iptvnator (ALT bug 44047)
 - epm repack xnview: improve packing requires
 Sat Dec 17 2022 Vitaly Lipatov <lav@altlinux.ru> 3.28.0-alt1
 - epm play r7office: fix install icons and associations (ALT bug 44093)
 - epm repack teamviewer: fix packing
 - epm repack rstudio: fix packing
 - epm repack meridius: remove unused discord integration (ALT bug 44251)
 - epm install: add --interactive support
 - epm ei: ask before install a package
 - epm play trueconf: drop unneeded workaround for install with --noscripts
 - epm requires: add support for --short
 - epm install: add workaround for --noscripts when using apt for additional requires
 Fri Dec 16 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.6-alt1
 - epm play ktalk: fix package name (ktalk2 now) (ALT bug 44230)
 - epm repack: clean created tmp dir
 - epm repack: fixes for ktalk (ALT bug 43486)
 - epm play: fix print description
 Fri Dec 16 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.5-alt1
 - distr_info: add --full-version
 - distr_info: fix Orel/orel checking for AstraLinux
 - epm repack vkteams: fix packing
 - epm play: add VK messenger
 - epm repack vkteams: prevent local .desktop creating (ALT bug 43779)
 - epm repack icq: prevent local .desktop creating (ALT bug 44250)
 - epm repack: ignore mono autoreq in generic-appimage.sh (ALT bug 43993)
 Thu Dec 15 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.4-alt1
 - remove dot in the end of wiki URL
 - epm play yandex-browser-codecs-ffmpeg-extra: fix repack
 - epm play: check if need update repo before install
 - epm play: use trap EXIT to remove tmp files
 - epm play pycharm-professional: fix install (ALT bug 44010)
 - epm play: print description only for applications with supported arch (ALT bug 43932)
 - epm play meridus: add support for install a given version
 - epm play: update flyview install
 - epm play flyview-server: add postinstall todo
 - epm repack: add support for pantum
 - epm repack brave-browser: fix repacking with broken cpio 2.13
 - epm repack: add support for brscanads2200ads2700w
 - epm repack: add libappindicator-gtk3 requirements for rustdesk
 - epm repack zoom: fix missed libffmpeg.so (ALT bug 44533)
 Thu Oct 27 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.3-alt1
 - epm repack spotify-client: fix icon packing error
 Sat Oct 15 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.2-alt1
 - epm repack pycharm-professional: rename icons to pycharm-pro
 - epm(): allow use it when run with pipe
 - epm repack pycharm-professional: fix packing
 - epm play flyview-client: fix package name
 - epm repack: fix icq packing
 - epm play okular-csp: remove repo also
 - epm repack ipera-client: filter out requires for embedded libs
 - eget: add --second-latest support
 - epm play opera: improve download latest available Linux version
 Mon Oct 03 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.1-alt1
 - epm repack Telegram: add Conflicts: telegram-desktop-binary
 - epm epack pycharm-professional: fix version 2022.2.2 packing
 - epm repack chromium-gost-stable: fix Name and Generic Name
 - google-chrome-stable: fix Name and Generic Name
 - epm repack chromium-gost-stable (ALT bug 43760)
 - epm repack wps-office: drop /usr/share/desktop-directories/wps-office.directory (ALT bug 43751)
 - epm play assistant: fix retrieving of a package URL
 Mon Sep 19 2022 Vitaly Lipatov <lav@altlinux.ru> 3.27.0-alt1
 - epm play: add RStudio support (ALT bug 43794)
 - epm full-upgrade: add update for flatpak and snap packages
 - epm: force disable verbose in quiet mode
 - epm repack slack: fix packing (ALT bug 43718)
 - epm repack: fix ipera-client (ALT bug 43761)
 - epm repack: fix ipera-mediaserver (ALT bug 43762)
 - epm repack onlyoffice-desktopeditors: pack icons (ALT bug 43713)
 Wed Sep 14 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.10-alt1
 - epm play: add meridius
 - fix non_interactive options
 - epm repack wps-office.sh: remove /etc/xdg/menus (ALT bug 43751)
 - epm repack spotify-client.sh: fix icon name (ALT bug 43720)
 - epm play yandex-disk: install also yandex-disk-indicator
 - github testsuite.yml: don't use yander mirror
 - epm play: add pycharm pro
 - epm play: improve pycharm (ALT bug 43613)
 Wed Sep 07 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.9-alt1
 - epm play: add Flyview (Ipera) server
 - epm play wpsoffice: fix return
 - epm-repack: fix packing dirs with spaces
 - epm play common.sh: fix typo (ALT bug 43706)
 - epm play assistant: add support for aarch64
 - epm repack teamviewer: add libminizip require (ALT bug 43723)
 Sat Sep 03 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.8-alt1
 - epm play: add wpsoffice
 - update embedded eget
 - epm repack common.sh: fix pack_dir
 - epm play: add FlyView client
 Sat Aug 27 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.7-alt1
 - epm repack fix pycharm-community on Sisyphus
 - epm requires: filter out rpmlib(*  for rpm
 - epm play: add trueconf client support
 Fri Aug 26 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.6-alt1
 - epm-epm_install: support mirrors
 - epm play master-pdf-editor: allow install on ALTLinux (ALT bug 43621)
 - epm play r7office: add support for many distro
 - epm play assistant: allow install on ALTServer
 - epm play myoffice: enable package scripts for removing too (ALT bug 43626)
 - epm repack common.sh: fix remove_dir (ALT bug 43613)
 - epm repack atom-beta.sh: fix (ALT bug 43614)
 Thu Aug 25 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.5-alt1
 - epm play: add VK Teams support
 - epm repack icq: fix description
 - epm repack skypeforlinux: fix packing (ALT bug 43615)
 - epm repack: fix packing scripts
 - epm-addrepo: fix typo (eterbug #15852)
 - epm repack common.sh: set PRODUCTDIR to PRODUCTCUR if empty
 - epm play: rewrite atom downloading and packing, add atom and atom beta support
 Mon Aug 22 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.4-alt1
 - change AstraLinux to AstraLinuxCE/SE
 Mon Aug 22 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.3-alt1
 - epm play: hide sputnik-browser (ALT bug 15741)
 - epm play: add Master PDF Editor
 - epm repack: fix /opt packing
 Sat Aug 20 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.2-alt1
 - add epm --short --version
 - epm-autoremove: enable real autoremove on yum based systems
 - fix $@ using for set vars (eterbug 15846)
 - epm repack icq: fix for ignore empty download
 - epm full-upgrade: do fatal on errors
 - epm play: return 0 if a package is already installed from the repo
 Fri Aug 19 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.1-alt1
 - add epm play virtualhere
 - more strong distro versions
 Thu Aug 18 2022 Vitaly Lipatov <lav@altlinux.ru> 3.26.0-alt1
 - fix: epm-download: always download rpm packages on ALT directly
 - epm play: add slack support
 - big revert "fix quotes in format strings"
 Thu Aug 18 2022 Vitaly Lipatov <lav@altlinux.ru> 3.25.1-alt1
 - epm repack icq: fix URL, ignore empty download
 - epm repack yandex-browser: fix provides
 - add epm play jetbrains-toolbox
 Thu Aug 18 2022 Vitaly Lipatov <lav@altlinux.ru> 3.25.0-alt1
 - epm repack: always set Epoche: 100 to override repository package
 - epm-search: fix support regexp not for apt only
 - epm-download: always download rpm packages on ALT directly
 - epm-tool: add json command support
 - epm play: add pycharm support
 - epm play: add icq support
 Tue Aug 16 2022 Vitaly Lipatov <lav@altlinux.ru> 3.24.3-alt1
 - epm_query_file: fix --short query for rpm
 - epm-query: fix --short query on rpm
 - fix docmd using (remove extra quotes)
 Tue Aug 16 2022 Vitaly Lipatov <lav@altlinux.ru> 3.24.2-alt1
 - fix quotes in format strings
 Tue Aug 16 2022 Vitaly Lipatov <lav@altlinux.ru> 3.24.1-alt1
 - epm-check_updated_repo: stop autoupdate repo info (too buggy)
 - epm play mssql-server: add Debian/Ubuntu support
 - epm-sh-functions: docmd/sudorun: use eval to handle env
 - epm install: separate install command for apt-dpkg and apt-rpm
 Mon Aug 15 2022 Vitaly Lipatov <lav@altlinux.ru> 3.24.0-alt1
 - epm play yandex-browser: add checking for yandex-browser-stable package from ALT repo
 - epm play opera: fix missed eget
 - epm play gitlab-runner: fix download on deb systems
 - epm-sh-functions: sudo -- don't allow vars, revert to just sudo
 - epm: add ACCEPT_EULA=y for install deb packages in non interactive mode
 - epm repack: set EEPM vendor for repacked packages
 - epm play geogebra: fix download on deb systems
 - epm play vivaldi: add snapshot support
 - epm(): run the script via bash
 Mon Aug 15 2022 Vitaly Lipatov <lav@altlinux.ru> 3.23.4-alt1
 - epm play: add support for opera beta and opera developer
 Mon Aug 15 2022 Vitaly Lipatov <lav@altlinux.ru> 3.23.3-alt1
 - epm-release_upgrade: remove conflicts branding file before upgrade
 - epm-repack: add support for EPM_REPACK_SCRIPTS_DIR
 - epm play anydesk: no strict version
 - epm play: add opera support
 Fri Aug 12 2022 Vitaly Lipatov <lav@altlinux.ru> 3.23.2-alt1
 - distr_info: add --codename support
 - epm: repo addkey support (add gpg key for a repo)
 - epm play: add rustdesk support
 - epm play: add Okular GOST support
 Fri Aug 12 2022 Vitaly Lipatov <lav@altlinux.ru> 3.23.1-alt1
 - epm play ktalk: add pre requires (ALT bug 42558)
 - common.sh: create shell wrapper with shebang (KDE runs Exec via execvp) (ALT bug 42641)
 - epm repack: fix shebang for obsidian and chromium-gost-stable
 - epm-query_file: follow a link ever if the link is not from a package
 Thu Aug 11 2022 Vitaly Lipatov <lav@altlinux.ru> 3.23.0-alt1
 - epm-repack: fix package name-version before convert
 - epm play Telegram: restore Conflicts: telegram-desktop
 - epm-repack: on deb convert to an intermediate rpm package if we have repack.d rules
 - epm play.d/common.sh: use mirror.eterfund for eepm.ru too
 - distr_info: add error about unknown option
 - epm play: allow direct run the scripts
 - epm play sputnik-browser: cleanup, add verbose checking URI accessible
 - epm play assistant: add URI checking and fix download on Ubuntu
 - epm repack: use BIGTMPDIR conception (ALT bug 43491)
 Wed Aug 10 2022 Vitaly Lipatov <lav@altlinux.ru> 3.22.3-alt1
 - epm play: add MyOffice support
 - epm repack.d: fix quotes
 - epm-download: fix permissions for downloaded file
 - epm install/repack: big refactoring to support rpm/deb platform in common way
 - epm-install: check if install by command
 - epm play: add mirror check for yandex-browser-codecs-ffmpeg-extra
 Sun Aug 07 2022 Vitaly Lipatov <lav@altlinux.ru> 3.22.2-alt1
 - repack.d/common.h: skip *_file/dir with empty arg
 - repack.d/common.h: add filter_from_requires function
 - add repack.d/rudesktop.sh
 - epm repack.d: use filter_from_requires
 Sun Aug 07 2022 Vitaly Lipatov <lav@altlinux.ru> 3.22.1-alt1
 - epm play rudesktop: fix eget using
 - epm play assisant: fix locale for cyrillic URL
 - epm-repofix: fix for Sisyphus
 - epm play: add gitlab-runner install
 - epm play code: fix link creating
 - epm play: fix sublime-text packing
 Sat Aug 06 2022 Vitaly Lipatov <lav@altlinux.ru> 3.22.0-alt1
 - generic-appimage.sh: drop MacOS only catalina dir (fix for balenaEtcher)
 - distr_info: strip long version for ALT Workstation
 - epm checkpkg: add --all support
 - epm play: add --force for --update support
 - epm play: add --list-installed-packages
 - repack.d/generic.sh: more common python -> python2 shebang suport
 - epm play: add signal messenger support (thanks, george@)
 - epm autoorphans: skip packages installed via epm play
 Mon Aug 01 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.8-alt1
 - eget: fix making file url from site url and filename
 - eget: add --check support for check url if accessible
 - play.d/common.sh: use eget --check in check_url_is_accessible
 - play.d/common.sh: add update_url_if_need_mirrored
 - epm play yandex-browser: use mirror.eterfund.org as mirror too
 Sun Jul 31 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.7-alt1
 - epm-install: yum does not support --allowerasing
 - don't expand package names on ROSA
 Sat Jul 30 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.6-alt1
 - epm-autoremove: add --auto support for apt
 - epm-remove: add missed --auto support for apt
 - epm-install: add --allowerasing for yum/dnf install
 - epm-query: don't use Epoche for hi level form
 - distr_info: use RELS name for ROSA Server, fixes for ROSA
 - eepm.spec: provides/obsoletes epm only on ALT
 Thu Jul 28 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.5-alt1
 - epm-sh-functions: add sudo_allowed
 - epm-filelist: fix sudo checking
 - zypper: add --non-interactive support
 - epm-install: always use apt for install deb packages
 Wed Jul 27 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.4-alt1
 - distr_info: add support for Debian GNU/Linux
 - epm print: disable name from package name guessing
 - epm-addrepo: add support for install powertools on RHEL family
 Tue Jul 26 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.3-alt1
 - epm-check: add support for --auto and --verbose
 - epm-install: revert to old .deb install way
 Tue Jul 26 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.2-alt1
 - distr_info: fix for RHEL
 - distr_info: stop detect snappy
 - epm-install: always use apt-get for install .deb file packages
 - epm print: fix print name/version/release by string
 Tue Jul 26 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.1-alt1
 - epm play wine: remove wine-gl and wine-twain packages
 - epm-install: apt need ./ path for install deb packages
 - epm play yandex-browser: add fallback for yandex-browser source URL
 Mon Jul 25 2022 Vitaly Lipatov <lav@altlinux.ru> 3.21.0-alt1
 - epm-update: cd / before apt-get update
 - distr_info: improve override support
 - epm-print: fix arg for distr_info
 - epm-check: add check_updated_repo before fix
 - epm-install: use apt-get install as fallback when install files with dpkg
 - epm repack: fix repack/install rpm on a deb system
 - epm-query-file: fix --short for apt
 - epm-sh-functions: disable eatmydata using
 Tue Jul 19 2022 Vitaly Lipatov <lav@altlinux.ru> 3.20.0-alt1
 - epm play: skip update for hidden packages
 - epm play.d: add rudesktop support
 - epm-full-upgrade: add epm clean after all
 - distr_info: big OS detection rewrite (based on /etc/os-release)
 - epm-release_upgrade: allow upgrade/downgrade to c9
 - epm-print: fix typo with rpm_query_package_format-field

Ошибка воспроизводится.

- Версии пакетов:
eepm-3.34.1-alt1.noarch
eepm-repack-3.34.1-alt1.noarch
eepm-yum-3.34.1-alt1.noarch

- Стенды:
kworkstation-10.1-x86_64
education-10.1-x86_64
education-10.1-kde-x86_64
workstation-10.1-x86_64
server-10.1-x86_64

- Шаги для воспроизведения:
1) # epm play vkteams
2) $ vkteams
3) Найти VK Teams в меню приложений.

- Фактический результат: в меню приложений две кнопки VK Teams.

- Ожидаемый результат: в меню приложений одна кнопка VK Teams.

При первом запуске приложения для пользователя создается vkteamsdesktop.desktop

До запуска vkteams:
$ ls -l ~/.local/share/applications/vkteams* /usr/share/applications/vkteams*
ls: невозможно получить доступ к '/home/test/.local/share/applications/vkteams*': Нет такого файла или каталога
-rw-r--r-- 1 test test 431 мар 28 12:29 /home/test/.local/share/applications/vkteamsdesktop.desktop

После запуска vkteams:
$ ls -l ~/.local/share/applications/vkteams*
-rw-r--r-- 1 test test 431 мар 28 12:29 /home/test/.local/share/applications/vkteamsdesktop.desktop
$ l /usr/share/applications/vkteams*
-rw-r--r-- 1 root root 327 мар 28 12:28 /usr/share/applications/vkteams.desktop

EPM package manager version 3.57.3

Стенды:
workstation - p10
simply - p10
regular - Sisyphus

Ошибка не воспроизводиться. До запуска и после запуска приложения vkteams в меню запуске приложений одна кнопка vkteams.