22.04 to 24.04 upgrade automatically removed numerous user-installed applications and left broken pinned launchers

[sprfolker]

Complaint / bug report

Summary

During the Pop!_OS 22.04 LTS to 24.04 LTS upgrade, the upgrade process automatically removed numerous user-installed desktop applications. Afterward, KDE Plasma retained pinned entries for the removed applications, but displayed them as blank document icons because their .desktop launchers no longer existed.

This caused significant disruption. An operating-system upgrade should not remove a large collection of recognizable end-user applications without an unmistakable warning, a complete removal list, and explicit informed confirmation. If removals are unavoidable, the upgrader should preserve a machine-readable restoration list and present clear recovery instructions afterward.

Environment

• Upgrade path: Pop!_OS 22.04 LTS to Pop!_OS 24.04 LTS
• Upgrade date: September 7, 2026
• Current OS: Pop!_OS 24.04 LTS (noble)
• Desktop: KDE Plasma
• Current kernel: 7.1.5-76070105-generic
• Installed pop-upgrade version: 1.0.0~1778861967~24.04~f2903ce

Evidence from APT history

/var/log/apt/history.log records the following upgrade-related command at 16:01:40:

apt-get -y -o Dpkg::Options::=--force-confdef
  -o Dpkg::Options::=--force-confold
  --allow-downgrades --auto-remove remove ...

The explicit removal target list included these user-facing applications:

• AppImageLauncher (appimagelauncher)
• balenaEtcher (balena-etcher, balena-etcher-electron)
• ChatGPT (chatgpt)
• checkra1n (checkra1n)
• Claude Desktop (claude-desktop)
• Element Desktop (element-desktop)
• Ferdium (ferdium)
• FirefoxPWA (firefoxpwa)
• NinjaRMM/NinjaOne NC Player (ninjarmm-ncplayer)
• Proton Mail (proton-mail)
• RustDesk (rustdesk)
• ServerPlus Default and Helpdesk (serverplus-default, serverplushelpdesk)
• Signal Desktop (signal-desktop)
• Sublime Text (sublime-text)
• Tailscale (tailscale)
• Waydroid (waydroid)
• Cisco Webex (webex)

It also removed Node.js/npm and many dependencies. The application removals above were not inferred from missing icons: their package names are explicitly present in the APT history's removal command and resulting Remove: record.

Steps that produced the problem

1. Start with Pop!_OS 22.04 LTS with third-party applications installed and pinned in KDE Plasma.
2. Perform the offered Pop!_OS upgrade to 24.04 LTS.
3. Log into KDE Plasma after the upgrade.
4. Observe that numerous applications are no longer installed.
5. Observe blank icons where their pinned launchers remain on the panel.

Actual result

• Numerous user-installed applications were removed.
• Their KDE pinned-launcher entries were not cleaned up or migrated.
• The upgrade did not provide a useful post-upgrade list explaining what had been removed or how to restore it.
• Applications now have to be identified and reinstalled individually.

Expected result

• Preserve compatible third-party applications whenever possible.
• Before removing user-facing applications, prominently show the complete list and require explicit confirmation.
• Clearly distinguish applications from obsolete dependencies and kernels.
• Save and display a post-upgrade removal/restoration report.
• Either preserve valid pinned launchers or clearly identify launcher entries that will become invalid.

Requested resolution

Please investigate why this upgrade path placed these applications into an automatic removal transaction. Please also change the upgrader so future users receive a complete, understandable warning and restoration report before and after any application removals.

Personal impact and comment

On a personal note, I find it absolutely ridiculous that Pop!_OS would remove applications on its own without any clear warning or disclaimer in the changelog, and without presenting a warning, removal list, or permission prompt during the upgrade itself.

Some of the removed applications are work-specific tools that I can obtain only through my employer. As an IT administrator, I now have to begin my workday by contacting my supervisor and arranging to have those applications restored. This is not a minor inconvenience; it directly disrupts my ability to do my job.

One reason many of us switched from Windows to Linux is a principle I often describe this way: Linux does what you tell it to do and returns what you ask of it. It does not burn the house down while trying to put out a fire. That was certainly not my experience with this upgrade.

I am deeply disappointed. I hope the Pop!_OS team takes this seriously and changes the upgrade process so that users receive a prominent warning, a complete list of applications that will be removed, and an explicit opportunity to cancel before removal occurs. This is especially important because some of the affected applications were originally installed through the Pop!_Shop itself.

Related report

A related open report appears to cover the stale launcher symptom:

• 22 to 24 upgrade: icons for uninstalled apps remain #381

This report additionally documents the broad application-removal transaction and requests adequate disclosure and restoration support.

[leviport]

Sounds like this might be a duplicate of #376

It is intentional that third-party PPAs are removed and applications from them are uninstalled. There is no way to guarantee the suitability of third-party PPAs for the new release, so this is necessary to prevent much uglier failures.

There is a warning about this in the upgrade dialog, which can be seen here: #379. I'm not sure whether it's feasible to add a list of applications that will get removed, but that could be its own feature request.

Flatpak versions of applications survive upgrades, so it may be worth considering using those versions instead.

On a personal note, I'm sorry to hear this upgrade was unpleasant for you.