A freshly created Ardour6 project imports an audio file with ‘Copy to session’.
After Save, in the .ardour files there are absolute path names in audio-search-path and midi-search-path.
After Save As with copying media to new session, in the new .ardour files audio-search-path and midi-search-path are empty.
I think that audio-search-path and midi-search-path should always be empty as long as imported files are copied into the session.