My cowl flap motor went a couple years ago.  I can't really tell you why but the A&P felt that the most likely problems was stripped gears.  For quite some time I tried to find a cowl flap motor.  Mooney said $1,000 but none are available.  We went another route and tried to put in a manual cable system similar to the 231 version but the cowl flaps aren't the same and the original cable and two subsequent attempts have failed.  I don't think the first cable was strong enough to pull the flap