To clarify, when you say that your thumb hole is usually drilled right below your fingers, do you mean in line with the your fingers, or do you literally mean right underneath, meaning that there really isn't a span of any sort? I ask because that will determine whether or not your ball is legal.
As others have said, as long as you show that you can reasonably use the drilled thumb hole to grip the ball, you are good. If it's drilled at a reasonable span length beneath the finger holes, you obviously would be able to put your thumb in it and attempt to throw a shot if you wanted to. If it's directly underneath the finger holes, you wouldn't be able to do so, and, as she stated, the ball would be illegal.
If it were drilled illegally, I can see the reasoning for the DQ; however, I don't really understand going so far as to say she's going to try to have your achievements taken off the books. That part sounds a bit strange to me. The whole reason for these rules is to try to keep up with keeping the playing field fair now that we've got a lot of no-thumbers and two-handers in the mix. As some of you may have remembered, I bowled two-handed as part of a USBC research study a few years back. Personally, I think they should either make people designate one-handed or two-handed, thumb in or no thumb the way they designate RH or LH, or they should just let you throw the ball any damned way you can as long as the ball is drilled legally. I've always thought that if I'm good enough to switch hands, why shouldn't I have an advantage?
But back to the point, I don't see any possible way she can have your achievements taken away. As for the tournament DQ, if you can prove that your can reasonably use that drilled thumb hole as a gripping hole, you got screwed over on that too. Sorry to hear it.