Originally Posted by shampoop
I don't see how a flush could ever stir up gunk.
Flushes are usually done by either removing an input and output line from the trans and hooking them up to a machine that discards the old stuff coming out and puts fresh stuff into the inlet. There is also a method that sticks a tube down the dipstick and flushes the transmission by sucking out the old and replacing it with new many times to where the old stuff gets so diluted that most of it's gone. It sucks from the bottom of the pan so it should do a pretty good job.
The pan only holds a portion of the fluid like maybe 1/4 to 1/2 of it, so dropping it doesn't get all of the old stuff out. I personally wouldn't worry about replacing the filter unless your old fluid was way overdue for a change and like black. Either way make sure whatever fluid you put in is synthetic. Heat kills transmissions and synthetics deal with it a lot better.
A flush is moving fluid through the trans under greater pressure and with more velocity than is typical. A flush is designed to stir up shit in the trans which is fine if you have a small amount of grime and have been doing the service every 30k. If you've never done it or don't know if the previous owner did it then you might have a lot of grime that could be dislodged and get stuck in a passageway causing rough shifting.
To be safe I would drop the pan, replace the filter, fill with fluid, and then at my next two oil changes drain and fill from the plug. I would use the recomended Toyota fluid.