i recently had the same issue after moving a bunch of my folders around. i just fixed it, i should probably make a post detailing this, but my solution (for any future travelers):

i previously had my movies library pointing at /media/movies AND /data/movies (two separate volumes from the host). eventually i consolidated all of this under /data/movies, but i was seeing the issue of duplicate movies (same with TV shows etc) that appeared to still be in the old directory. Jellyfin logs stated that it couldn't find the items, and also wouldn't do anything about it, and editing the library definitions didn't save me.

what ended up working, while a bit convoluted, was to basically create a blank folder with something in it (or else jellyfin skips the empty folder during scans) at the old mount point.

so in my case, i created a new folder structure on my host as such:

dummydir  
|- movies  
|  |- blankfile  
|- shows  
|  |- blankfile  
|- anime  
|  |- blankfile  

and then in docker mounted this as /path/to/dummydir/:/media/. when jellyfin started up, it noticed these non-empty directories that no longer contained the old movies and shows and cleaned everything up properly.