There are a couple of circuit boards in the roof to control the fan functions, and there a several different model levels of fantastic fan , but to keep running with the fuse removed .
If you have info on the fan ; owners manual , model number; give Fantastic Fan a call and see if they can help.
Is it possible that the auto/ manual , knob got pulled to the manual ( down ) position , and just needs to be pushed up to re-engage the drive?
Man, everyone types faster than I do.