I haven't gone and had a look at how MusicBee behaves on my side for the above scenario, but:
If those missing tracks have been found and located in the main library, I don't understand how MB would still deem them "missing" in the playlists.
Unless it's a bug or those tracks in the playlist were previously dragged and dropped from outside MB and not necessary sourced from the existing ones in the library.
What MusicBee version are you using?
I'm sure you've restarted and rescanned MB since posting this - are the tracks still marked as missing?
And it goes without saying that next time, if you wanna move any files, do it within MB itself so that it knows the new location (File Organizer).