There is always the chance that doing a flush could knock something loose and make it worse. Personally I think dropping that pan to inspect the magnet, changing the filter and fluid is perfectly safe. I made up a new article for changing the filter and fluid. http://www.gmforum.com/t278423/
I've done several of these, and 2 of them had transmissions that would not go in to gear cold. After changing the filter things worked fine. If the filter is plugged or really restricted it will prevent the fluid from flowing and causing the pressure to drop, making it harder to engage the clutches.