That is kind of a touchy subject....I have had many people/sites say not to do a restore after a ROM update because it will over-write the update, but then you have some updates (the last couple from VZW that tell you to do just that....create a backup just in case.
Also (I can't speak for any other service than VZW here) all the upgrades I have done (3) have only upgraded the POM, and left everything intact, so I never had to do an update.
Just my experiences!!