Two Flatpak entries with the same friendly name may refer to different installations or branches. Updating one entry does not establish that the application you normally open came from that entry. Build a precise inventory before removing what looks like a duplicate.

Record more than the display name

Run flatpak list --app to list installed applications. Flatpak's list command includes both per-user and system-wide installations by default. Its --user and --system options narrow the view, while --installation selects a named system installation where one is configured.

Use flatpak list --app --columns=application,version,branch,origin,installation to show those identity fields. Record the full application ID and distinguish a testing branch from the regular branch. The origin identifies the supplying remote; a familiar icon does not identify that source.

Use flatpak info for the intended application with the same installation scope, adding its branch when necessary. Keep the resulting identity with your note. If an organisation configured an additional installation, do not collapse it into the default system entry merely because both are available on the computer.

Connect the inventory to the actual workflow

Save open work and note the version shown by the application you normally use. Compare it with the inventory and ask the maintainer to identify its launcher when the relationship remains unclear. A menu entry and a package listing are different pieces of evidence.

For example, an intentionally installed preview may be useful for testing a document format while the ordinary release remains the work application. Preserve that distinction rather than uninstalling whichever entry looks older.

Apply an agreed update to the intended installation and branch, then reopen that application and test a representative document. Confirm its displayed version and required extensions or settings. Do not remove another installation until its users and data requirements are understood.

The finished record should identify the exact app, branch, source and installation used for normal work. This gives future updates a clear target and prevents a successful update message from being mistaken for proof that every similarly named copy changed.

Sources: Ubuntu documentation, Ubuntu documentation.