Backing up problem

I want to backup my DB, but it won’t let me repair the error it finds (647 files missing). In general, I think I’ve made a dog’s breakfast of my db. Any suggestions in organizing it properly and cleaning things up? Sorry for the vagueness of this question…

File > Verify & Repair Database… lists all missing items in Windows > Log. Afterwards you can trash or reveal them via the contextual menu.