I had this situation just before the '09 season tipped off. I got mixed responses about how to handle this situation properly. So I contacted our local rules guru for clarification:

If the net flips up we are obligated to make sure it is in its normal position because by definition a goal cannot be scored unless the ball passes through or remains in the basket. If we need to stop play, we stop play to fix it.

When it appears to be an ongoing problem, having someone free the net in transition was an acceptable solution as well.