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.
I suspect the scanner has some bug in it related to local assets (fanart, poster, season, theme etc…) where plex gets into some error condition and it no longer picks them up.
The rename - scan / metadata refresh - rename again and final scan / metadata refresh of the local assets seems to forces plex to pick them up again.