C'mon, man. Although it IS cool you asked, because too many people take too much shit for granted just because they read it on a messageboard. BUT--no one ever seems to ask the people crapping on Lucas for proof that their rumors have any merit
Check www.jwfan.net. They've got some very detailed stuff. The scenario you're describing is the scoring of The Phantom Menace, which had it's 6th reel scored twice due to Lucas' re-editing, and then the chop job came when Lucas decided, last minute, to re-edit the 6th reel ONE last time. Couldn't get Williams in to re-score one last time, so the music took the hit. That was pretty much all Lucas' fault, and word is his 3rd edit of that reel didn't even really improve on the 2nd, which left the lightsaber fight and Space battle alone, mostly, and tended to crosscut more between the Naboo battle and the Princess storming the castle.
For AOTC, they knew post production was going to go down to the wire again, (Lucas had just recently created and inserted the droid sequence late in Post) so they talked beforehand, and decided they'd just leave most of the clone battle blank, and Williams' producer would cut music together from TPM and AOTC. So Williams didn't even write any music for that sequence. So the blame for the choppy music editing on that one goes to Williams' producer, who really didn't do a good job transitioning between cues at all. There was no music "rejected" by Lucas, he doesn't do that. He has, of course, chopped up cues and cut some short, going back to Empire Strikes Back, and including "The Droid Foundary" (which is one of Williams best cues, in my opinion) in AOTC, but I dont' think there's ever been an example of Lucas going "That cue sucks balls, go write another one."
the stories were pretty well known amongst the score fans, but JWfan.net did a really good job of consolidating and compiling it all on their site.