frustrating issue... i never let any app flinger my folders.
if all is tagged well u could have organized the files back to the other drive using the monkey, u just have to insert a folder mask that suits u and veryfy in the preview that all is going as aspected before hitting the go button
an example is
d:\Music\$if(<Album Interpret>,<Album Interpret:1>,<Interpret:1>)\$if(<Interpret>,<Interpret>,!divers)\$if(<Album>,$if(<Jahr>,<Jahr> ,)<Album>,)\$if(<Song#>,<Song#:2> - ,)<Titel>
another hint when u copy by hand and plan on using the find missing/moved files feature.
delete the old entries from the mm database (archive > files to edit > dead entries) to avoid possible issues (potential messes up some tracks that have same hashes but are indeed different tracks).
ignore that if u manually move the files and normally add them.