I have a copy of a film, but Plex has wrongly labelled it as the remake rather than the original version (both titles are identical). Presumably Plex can also recognise the older version of the film too but has chosen to list it as the newer version in this case.
If more than one film is found by the same title when refreshing the library, if there is the possibility of plex getting it wrong perhaps you could offer the opportunity to the user of selecting which one it is during that process? (assuming it's not already). Since reboots seem to be fashionable these days it might end up being useful.