If a transmission is on it's last leg, changing the fluid or flushing will usually kill it, since the new fluid won't have remains of suspended friction material. A transmission in that sad of state would have needed to be replaced or rebuilt anyway.
Regular maintenance on a good transmission won't hurt it. I had my 4R100 flushed/filter change last year without incident, and the truck is daily driven with a 8,000 lb curb weight.