Bummer, some of those LFOs made a big difference in a few patches. Will have to discuss with CW...
That's always been a difficulty with Rapture. I don't know if Rene realized how much that feature would be exploited. At FiSound, we made the UD-LFO install optional. Some other Expansion Packs just overwrite the 80 slots. Neither solution is perfect, and - as you've mentioned - some presets will become unrecognizable.
Sure, there are workarounds. Not exactly transparent to the end-user. If there is ever a Rapture 2 release, this is one of the features that really needs some re-tooling. The entire set of LFOs is scanned at launch, so you would think there'd be a way to flag an appropriate set. But with multiple XP sets installed, an LFO would almost have to be saved within a specific preset itself.