My experience in this area is limited to GM cars but I haven't had any trouble. I never do the "Jiffy Lube" type flush however. My indy drops the pan, changes the filter then tops off the level. He then disconnects the line going to the tranny cooler and starts the engine. As the fluid is pumped through the torque converter and out the bleed he replaces it with fresh fluid until the exiting fluid runs clear. Shut it down, button it up and adjust the level until correct.
This would not harm the seals unless fresh fluid is bad for them.
