There are many ways a sub can be damaged from clipping. ripped spiders, broken tinsels, fried coils.
I doubt the sub was pushed passed its mechanical limits, I know someone pushing 4 type r 10s with around 4-5 thousand rms, and they are taking it. Only problem they had so far is that the glue let loose on the surround where it was adhered to the basket.
Bass boost all the way down, and 3/4 gain is still most likely clipping the amp, and the low bass boost should not be compensaited that much with the gain.