The iOS 5 beta 4 over-the-air firmware update will not work on jailbroken devices, according to MuscleNerd.
The 5.0b4 OTA update won't work on JB devices due to an explicit check of /Applications..almost like a present from Apple
they check to make sure /Applications is a real directory, which it isn't in a stashed jailbreak (not sure how unionfs would act)
While this sounds like a bad thing, it may actually help in preventing accidental updates which often lead iPhone users to lose their jailbreak or unlock.