Breaking in a sub is a completely absurd excuse for what happened. That isn't even a remote possibility. I have no doubt that they are right about the voice coil frying, though.
When you break in a sub, the result is usually a small (very small) change in the T/S parameters.
Breaking in a sub is slightly more useful than painting the edges of your CDs green to get better bass response, or using $500 speaker wire. It however much more useful than anything Bose has come up with.
btw, I'm glad they are helping you out!
