So I had a look at Pumbaa's files for this asset, and had a couple things to write up about. I edited the lowpoly to match back up to the high as i think you edited it, trying to "fit" the high inside it. No need to do this, this is what the cage/envelope is for, and doing this sort of tweaks is only going to make things…
Pumbaa, looks like you got the skewed projection issues solved, really all you need to do is run this script now to set hard edges via uv islands: http://www.polycount.com/forum/showthread.php?t=52722 As long as your uvs are set up well(IE: the end cap is on its own island and not welded to the side of the other bit) this…
You could leave your LP as separate objects matching the HP, do the animated break up, copy them all, then use the collapse utility on the copies to get a single mesh for rendering. Keeps the animation on the object level, and gives a single map result. Albeit that would be a (scriptable) extra step for rebakes.