Hmm, I don't think Freeway knows how to handle files that have been deleted. I'll work on this when I get some time, but for the time being, erase the library.ini and rebuild from scratch. It won't have to download album art again, so it should be relatively quick.
Also, does it handle file deletion? Because I recently deleted a directory from my mp3 folder, and FW still has the files in its library. Thou, when playing, I get "error 76, path not found". I tried rebuilding both winamps library (witch does not contain the files any longer) and FWs database (witch does still have them).