Most of the tranny flushes that cause problems are the ones that also run a cleaning agent between the old oil out and the fresh oil in. A simple swap can also cause problems if the tranny is too old and the fluid has never been touched since it can break things lose that were gunked into place. Regular flushes won't hurt anything as long as the filter is changed once in a while as well. I still prefer the pan drop method since I can do it at home, but a simple flush shouldn't cause problems in an otherwise healthy tranny.

THe flush thing is a myth, and it'* been debunked by Myself, Willwren, 2 very reputable trans shops, and others.