Scanning library overwrites custom metadata of existing films - please help

Inspect the content of the guid="... property in the Plex XML info of this movie.
Does it say local?
Then you have to manually match the video to the ‘Personal Media’ agent, by doing this:
start a Match/Fix Match procedure https://support.plex.tv/articles/201018497-fix-match-match/
click on ‘Search Options’
select as Agent ‘Personal Media’
Search
click on the sole search result