leveraging facts and myths...
Here's a sticky that describes some info about trans flushes.
http://www.explorerforum.com/forums/showthread.php?t=161337&highlight=trans+fluid+flush
I would tend to agree... a flush can be good or bad. I think if done regularly from when new, a flush could be advantageous to keeping the system clean and the fluid healthy. However, with older transmissions that have seen a lot of use, or haven't had frequent fluid changes or flushes, to a certain degree they are happy running as they are. A fluid flush, and the detergent capability of the new fluid or any additive can help dislodge sediment or varnish, which otherwise would stay happily in place. In low-tolerance valves, these particles could cause problems.
From personal experience - I did a fluid flush on my own (the at-home method described in several other posts). It seemed to work well, but I saw trans failure about 25K miles later. Was it to blame? Maybe, maybe not. The failure mode was a combination of a sticking 1-2 shift solenoid as well as a couple of broken bands. (I'm no trans expert by any means)... and the trans had about 130K miles on it... in my experience, about the max for the 4R55E without meticulous maintenance. I had done standard filter/pan drops before, so I was only getting about 1/3 of the fluid.
I'm going to roll the dice with a flush this week... the first on the new trans after about 25K miles. Hopefully it hasn't had a lot of time to gum up, and it should treat it well. Plus, I just finished doing about 1000 miles of heavy towing this weekend, and the fluid is looking pretty dark after that. Crossing my fingers that all goes well, and that my logic works that this trans should be able to handle a flush, since it's reasonably new.
WRT the torque converter - I too have heard if you do the flush yourself, it is imperative to maintain the fluid level as much as possible - you do NOT want to run it dry. That's how the pump systems work: fluid in = fluid out, so you maintain correct fluid pressure.
My personal recommendation? If you've got 80K or more on a trans, and have maintained it only minimally, you may want to just do a pan-drop and replace some of the fluid... maybe do it a few times successively over the course of 5000 miles to kind of do a "slow" flush, which won't shock the system so bad if you have a lot of mileage gunk built up in it. But that's just my $.02.