You should delete/move music files within the MusicBee interface, not with Windows File Explorer, so MB knows what happened and can modify the library accordingly. You can move them using the "Computer" interface in the left sidebar (select it in Prefs/Layout(1)). If you are deleting files from your library and computer, right-click them in the Music tab and choose "Delete--From Library and Computer."
You can get rid of the deleted "ghost" file entries that still show in MB by using the menu option Tools->Advanced->Compress Library.