So you can load both folders into Jaikoz and set Preferences:Local Correct:Delete Duplicates to It has the same Acoustid as another song but I guess the problem is you cannot choose which of the two songs to delete.
I would expect it would either always delete the right one (unmatched music) or the wrong one [sorted music), so have you actually tried it, remember nothing is actually deleted until you save changes so you can safetly check this.
If it is the wrong one you could use Filter:Filter AcoustIds: Duplicate AcoustId this will then only display files that exist with more than one file having the same duplicate Acoustid . Then you can sort the Sub Folder field (will be hidden by default) so that all the duplicates found in Unmatched music are together, the you can select them in the rownoumber column and use right click menu Delete:Delete Files to delete them.