I believe this is expected since those GUIDs are based on file paths. If a file is removed and then added back with the same path, Jellyfin can link the watch status again. However, if the path is slightly different, it cannot match it up again.

there are 3 different entires for the same file in the db, which is odd, it honest feels like a bug. I could really do with this being attaching to the movie/episode rather than a filename, it feels like an odd decision with the refactor. Maybe if this is expected, I can requeest a feature for options.