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Created attachment 1721558 [details]
Patch fixing the problem

If you have the same ref (com.redhat.Platform) in two remotes:

 * In a system remote, uninstalled
 * In a user remote, installed

Then trying to update or remove the installed package confuses GNOME Software because when processing the Flatpak transaction it looks up the *uninstalled* application rather than than installed application.

This was fixed piecemeal between 3.36 and 3.38 (https://gitlab.gnome.org/GNOME/gnome-software/-/commit/ae8f7e34cbc85174310849868f6bc61e6a3154ed and part of https://gitlab.gnome.org/GNOME/gnome-software/-/commit/dd100c88d0fe1dbdc271fb685cb34b5fe791c91c) 

I'll attach a patch here that has what is needed to fix this.

Thanks for the patch. I guess I can devel-ack it, due to the patch available.

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory (Moderate: GNOME security, bug fix, and enhancement update), and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://access.redhat.com/errata/RHSA-2021:1586