My dealer did a flush on mine a couple years ago and I noticed a difference in the shifting for the worse right away. Then it started making some noise. Long story short, they had to warranty a transmission rebuild.
Obviously something went wrong with the flush, they denied the fact the entire time that their mechanic ever did anything wrong, and all I asked them was to make sure whomever worked on my truck that day never does another flush for anyone else.
I brought it in on a Saturday originally, so maybe I got stuck with the pimply face lube boy and not their transmission technician. Maybe the new fluid level was low, maybe somehow some debris got flushed into the tranny I don't know, I forget exactly what they had told me what went wrong and I'd have to dig through my stack of old paperwork on the truck and see what they claimed on the diagnosis and service record.
They were very good about the rebuild process all in all and walked me back there, introduced me to their transmission mechanic who showed me around my pile of parts, and reassured me I was in good hands. Seeing a brand new GT350 up on the lift next to mine getting a clutch warrantied with only a few thousand miles, made me feel a little better.
It's been tens of thousands of miles since then and the transmission has been totally fine, and my truck sees a lot less miles these days, but I think I'm staying away from another flush ever lol.