Good luck with that!!! If your tranny [censored] the bed due to a flush, there's not a snowball's chance anyone will stand behind it. You see, with the miles that are on it, they'll blame on something, anything else to keep the blame and resulting liability off of them.
I don't care who does it, flushing a transmission with a machine is a bad deal. It takes any contaminates and forces them through the tranny at high pressure. before it exits to the machine. Another negative is that nobody will ever change the filter. So if it's plugged then your problem still exists. Bottom line, drop the pan, clean everything up and replace the filter. If you want to go the extra mile, add several quarts of ATF, then disconnect the return line (from the cooler), start the engine and let it pump the old dirty ATF out until it runs bright red.
BTW, "certified" is not a guarantee that you'll get a quality job. It does up the chances, but remember this... First and foremost, they are human and can make mistakes. Second, they are oftentimes on commission- and that puts pressure on them to perform at a high rate to make money.. Doing that leads to cutting corners. This I have seen with my own eyes. When corners are cut you will suffer, not them and rarely is it the other way around.