Killing the daemon using gpgconf is fine if you are aware you need to do it. We weren't, and I suspect few other users would be either.

I'm pretty sure what happens, but apparently I haven't been able to explain it clear enough. To reproduce you can do like this:

1. On an old machine having GnuPG version 1, e.g. Red Hat Enterprise 5:
   1. gpg --homedir $PWD/homedir --gen-key
   2. tar cf homedir.tar homedir/pubring.gpg homedir/secring.gpg
2. On a more modern machine having GnuPG version 2, e.g. Red Hat Enterprise 8:
   1. tar xf homedir.tar
   2. touch apa bepa
   3. gpg --homedir $PWD/homedir --sign apa # Does the migration, and signs "apa"
   4. mv homedir homedir.moved # Don't remove, just move
   5. tar xf homedir.tar
   6. gpg --homedir $PWD/homedir --sign bepa # This will fail as explaine in point 5 of the initial description

Neither gtk nor qt, I'm trying to run the curses version. (Would it help if I
tried the gtk and/or qt version?)