How can you change the filter with a flush? When you flush, you run the fluid back through the tranny, not through the filter first. If there is any debris, it will end up in your clutch packs, good luck with that. A complete way to do it would be pump the pan out with a cheap pump, drop the pan and change filters add back fluid, make sure pan is clean and then your flush would be less dangerous. Dealer flushes are inexpensive at oil stop, I think they quoted me 90 bucks which is really low, I would ask what that entails. But whatever, when you flush your transmission you are taking a risk to gain a benefit, at least realize that.
Chances are you don't have debris in the lines past the filter, that is what is lubricating. Chances are you do have debris before the filter, those machines will under pressure blow past that debris. Some machines are even worse, they send a solvent through first to dislodge the debris and send it the wrong way through the tranny. Reverse flush machines have been talked about forever, but I have yet to see or hear about one. If anyone knows, post that up.
Is running dirty/older fluid also a risk? Not much if that tranny is running under 200F. I get the urge to run clean fluids, but either bite the bullet and go allin, or take a pass would be what I would do.