I'm pretty sure this is not a bug.
Deleting/moving MB files/folders should always be done from within MB and -not- with File Explorer. Doing it outside MB is asking for trouble (as you saw) since MB has no idea where it went.
well when i press delete in musicbee it should delete the filter entry in musicbee... not?
that i have to create that folder again only so musicbee can delete it is a bit silly.
but it still showed up in the folder panel. even when i deleted it from the folder panel, on the next start it was there again
that musicbee wont find moved files is clear as crystal but in my case it only should remove a folder from the filter list.
but instead it shows a folder that does not exist anymore and ignores my delete command from inside musicbee.