All right, so I backed up the profiles with cp -r -d /nix/var/nix/profiles .
and then removed all the broken symlinks:
for f in $(find /nix/var/nix/profiles/); do if [ ! -e "$f" ]; then sudo rm $f; fi; done
Rebuilding the system now works.
So reading up on profiles, here’s what I think happened.
The store did not break, but I had lots of generations that broke because I forcefully removed a package that they still referenced.
Thanks for the help all! Really appreciate the quick responses
edit: for the .desktop entry not showing up in Gnome, I think it’s due to a change in the package so not Nix-related.