I've been running a Plex/jellyfin server for years and never had to rename any files. Don't do that. Match them in Jellyfin and leave the original filenames intact.
If you rename them, you can re-create the whole library with auto scan, which is nice.
Do you mean you let it auto-scan the wrong id, go find that wrong movie in your library, then manually provide an e.g. IMDb id, for every one?