You could always write a quick script that gets the current selection, does a Flatten action, then re-selects the original selection. Or was that one of the 5 workarounds?
Hey Don, Stop by, I've got a quick UV shift script I use that will move your selected UV's in one direction or another so that you can bake out normal maps, AO maps, or in your case, quickly select flattened UV's and then re-shift you're other UV's back to the 0,1 space.
You work at High Moon? Your Technical Director Randy Stebbing, does seminars for Autodesk, he's in pretty tight with some of the guys over there. Make sure he knows. When he talks, they listen. More then likely he'll write you a script (or have someone else with 5min do it) to fix it for now. As well as pass it along to…