@stevencas said:
Any ideas how to fix this issue which is causing a lot of unneccessary manual work?
More manual work. 
The Plex Dance ™
https://forums.plex.tv/discussion/277433/the-plex-dance
The purpose of this is to remove all cached metadata and xml data for an item that Plex usually keeps. This helps when you want to “start from scratch” for particular item
- move all files for the media item out of the directory your Library is looking at so Plex does not “see” it anymore
- update library ( scan for media items )
- empty trash
- clean bundles
- double check naming schema and move files back
- update library
