There were two ways to open the bomb bay doors: Electro-hydrolic and a manual crank.
Bombs had a pin that was tethered to the Bombay by cables. When the bombs fell, it pulled the pin. They also had a spring wound fuse and vanes that would unwind the spring as the bomb dropped. These were set to detonate the bomb at a specific altitude.
Bombs were normally released by electronically activated solonoids that automatically relased the bombs at a 1-20 millisecond interval.
If the electronics failed to release the bombs. The pilot had a mechanical release next to his left foot, the infamous "green apple". It was called the green apple because the screw on ball was green.
If either the hydrolics or crank could not open the bomb bay doors. The pilot would resort to the green apple. B-17s carried 6000 lbs. of bombs. Dropping this weight on the damaged bombay doors usually did the trick. It was clearly a last resort as it was not without significant risk!!
The answer to your question is YES, FLAK damaged the bomb bay doors quite often.