If you're reading this in the far future, the bug could have been fixed.
The behavior I observe happens on nixos-26.11pre1011622.a799d3e3886d.
Sometimes when I update the system or change how the font I use is packaged, Flatpak applications seem to dislike my actions and forget the font even exists.
As far as I know, Flatpak under Nix bind-mounts current fonts into the sandbox on launch, so if paths to these fonts change (even without their contents changing), the sandbox won't see these fonts.
The sandbox keeps looking at these paths because no one instructed it to recheck paths, or, in other words, its fontconfig cache went stale. The quick and dirty solution seems to be
rm -r ~/.var/app/*/cache/fontconfigand for the time being
(until #529277 is merged)
is more or less the only working solution
(apart from running fc-cache -f inside the sandbox).
Point for not bothering with updating every week (bitte nicht hacken).