No it won't, at least not by unticking it in the Scan folders for new files box, it will however remove them if they are moved out of the 'a' folder and then scan it (so potential solution is close MusicBee > rename 'a' to 'b' > create new empty 'a' folder > then in MusicBee scan > select remove missing files).
Possibly a better potential solution could be install a version of MusicBee Portable to a folder, you could then use that to edit the files instead keeping them completely separate from your library before you want to add them.