Kodi source problem

Hello.I have a Minix Neo U1.
I’m on the latest Kodi release.I have 2 external wd hdd’s that i use.One is for TV Shows ,One for Movies.I had them connected simultaneously on the minix.I added 2 separate sources and named them Tv Shows and Movies respectively.I did scan for new content and downloaded fanart etc.I plugged them off to add content from my pc,only to find out that all contents were mixed on both drives.Most were duplicated.I sorted them out,did a cleanup on the kodi without them connected.I connected them only one at the time now to add as source.Movies are ok.I unplugged Movies and did the same for TV shows.I’m afraid to plug them both at the same time in case everything gets mixed up again.Is there a way to avoid this?Thanks!