This may or may not be related however I suspect it might.
A while ago I experienced the same issue you are reporting but it was with poster artwork not themes. However, being local assets I think its related. See Some Posters not showing up and disappears - #13 by dokuro
I posted two workarounds in the thread above so maybe give them a try. If the second one ultimately does works then you can do something like this …
find <path or your movie library> -type f -name 'theme.mp3' -exec rename 's/theme.mp3/atheme.mp3/' {} ';'
This will find all theme.mp3 and rename them to atheme.mp3. At this point force refresh the metadata of your entire library. This forces plex to update and remove the local asset as its now got an invalid name. Then rename them back …
find <path or your movie library> -type f -name 'atheme.mp3' -exec rename 's/atheme.mp3/theme.mp3/' {} ';'
This will find all atheme.mp3 and rename them to theme.mp3. Now force refresh the metadata of your entire library and the scanner will pickup the theme correctly.
Best of luck and hope this works for you.
