I've never used the Zapper before but I think I want to start using it. However, I kind of like my Paralix and was wondering if you could use Elixirs on pets once they had been zapped?
Also, any suggestions before I start zapping? I read the FAQ about items in your inventory being able to be destroyed =S
Yup, you can still use any items on pets that have been zapped. You can also remove minions that have been zapped and they remain what they were zapped into (but other than the few exclusive minions, I'm pretty sure they only turn into slimes that are stat boosters), unlike Neopets.
You'll probably want to clear your inventory, yes. CWs can't be destroyed, and locked items are fine but other than that I don't know for sure what's safe and what isn't. Better safe than sorry though~