I had the transmission flushed and filled at 90K miles on my F-250. A week later, after few driven miles, it "lurched" as if going into passing gear and the Tow/Haul ON light started blinking. After the dealer scanned it, he first saw codes for a bad solenoid, then a bad EGR valve. When he dropped the pan he saw metal pieces. They road tested again and found it took off in 3rd gear and went right into 5th.
They recommend a refurbished transmission for $3200. Prior to any of the preventative maintenance, the truck ran great, no symptoms of any kind. I don't believe in coincidence.
They're not actually flushing the transmission. Flushing is a procedure which uses high pressure air and automatic transmission fluid to clear out unwanted debris and contaminated fluids from the transmission cooler and cooler lines. Flushing is only necessary after a catastrophic transmission failure, and performed prior to the installation of a new or repaired unit.
Recently, auto repair shops are selling more of a transmission fluid exchange program. Equipment is attached inline with the transmission cooler lines, and while the engine runs, new fluid is pumped in and the old fluid is pumped out. This procedure is replacing the old standby of dropping the transmission pan, changing the filter, and adding new fluid.
The advantage is replacement of almost all the fluid (10-15 quarts), as opposed to dropping the pan and replacing about 4-6 quarts. A large amount of fluid remains in the torque converter. A disadvantage to the fluid exchange is they typically don't drop the transmission pan to inspect for debris and replace the filter. The big reason behind the new method is profitability -- they do less and you pay more. The same results could probably be achieved by servicing the transmission the old fashioned way, just more often.
As far as your situation is concerned, the failure could have been induced by a number of catalysts. It may be a coincidence. Trust me, stranger things have happened. Was it the first transmission service? 90,000 miles is beyond the recommended interval. If the problem was indeed instigated by the service, it's gonna be tough to prove.
Incorrect or contaminated fluid may have been used, or small debris could have accidentally entered the system while the equipment was hooked up to the cooler lines. Either situation can damage seals necessary to apply internal clutches, possibly block hydraulic passages, or hang up a valve or solenoid (the EGR trouble code shouldn't be relevant to a transmission problem).
Have a friendly discussion with the service manager and see if he's willing to make a good faith effort on the cost. Next step would be a letter from an attorney, and the last resort a court of law. The dealership/manufacturer will drag it out.