HI Chaser!
The answer is rather complex.
No the fl;aps will not 'autoretract' on a real b-17.
If speed is increased over the long term with the flaps extended several things happen. First and foremost is you are overworking your power plants to maintain your desired airspeed.
Secondly damage to the flap retraction/extension mechanism can indeed result if airspeed is excessive.
Structural damage can indeed result if airspeed is excessive.
Flaps should not be deployed on a B-17 above 147 MPH indicated airspeed under ANY circumstances.
If you damage the extension/retraction mechanism the results can be catastrophic over the long-term. Short term results can be anything from they are now stick in the DOWN position to we now have one of em out there flapping in the breeze (it will eventually tear from the wing and may well take control lines, oil lines, fuel lines etc along with it if the mechanism breaks free of the flap control arm)
So the correct answer is between nothing adverse happening and a full blown system failure that results in a crash.
Airspeed, wind conditions, structural integrity of the systems, wear and tear over prolonged use, etc etc all play into the equation at some point.