It sounds like you're asking not whether EVPM scripts will run during USL failover, but rather whether the effects created by the scripts will persist. If that's a misreading of your question, then the below does not apply. Otherwise...
Short answer:
Yes.
Long answer:
EVPM converts the settings you specify in the .ini file (the "script") into a settings that are stored in the Exchange mailbox, either in hidden filter messages or as MAPI properties. The EV archiving tasks will read these settings when they process the mailbox, even if EVPM is never run again. That is to say, the settings specified in your EVPM script are persisted in the Exchange mailbox.
This means that even if EV's services find themselves on an alternate machines on account of USL/Building Blocks or cluster failover or poltergeist activity or whatever, the tasks should still find your EVPM-created settings waiting in the mailbox and abide by them.
--Chris
