bug#61882: profile is frozen / packages can't be installed

[Csepp]

(Jump forward a bit, this is a bit stream-of-consciousness-y, I wrote
things down as I was debugging things.  TLDR: profile got corrupted
somehow, it's not related to the packages themselves.)

Certain packages like flatpak do not get installed in my main user
profile for some unknown reason.
So far they are:
* gallery-dl
* flatpak
* emacs-org-roam

It has been happening for at least a month across several pulls.

If I export a manifest and load it in either guix shell -m or guix
package -m to a different profile, bin/flatpak exists, if I do guix
package -m without a profile argument or with the profile set to the
default user profile, bin/flatpak is missing.

The packages that are broken are always the same.

If I create a manifest with only the broken packages, guix package -I
reports exactly those packages, but when I look in ~/.guix-profile/bin
it still has a bunch of other packages in it.

So it seems the profile is frozen?  I have no idea how this could
happen.

guix package --list-generations reports three generations, but there is
only one generation in my home directory, called .guix-profile-1-link.

There is also a .guix-profile.lock, maybe that's related?
I see no lock for the other profile with the same manifest.

Removed the lock, tried guix package -m again, still don't have flatpak,
still only one generation symlink.

Deleted all the symlinks, ran guix package -m, now it works.

I'm gonna hold off on running the GC for a few days, if anyone has an
idea of where the bug is and wants me to upload some files, I can do it
until then.
For my own reference, this is the store item of the broken profile:
/gnu/store/0w3jxl95cchxn14zph3lmnqwmijf8971-profile