If I understand correctly:
* You installed MusicBee, which added your existing tracks to its library
* You deleted a heap of files in Windows Explorer
* Now you want to remove those (now) missing files from MusicBee?
Two ways to do this:
1. Manually: File > Rescan / Add files
with Remove dead links
2. Automatically every time MusicBee starts: Edit > Preferences > LIbrary
Select Check for updated files
and and remove dead links at startup
If I've misunderstood, then
Bee excellent to each other...