why would you want to do that?? IMO The only thing that immo does is piss the hell out of you since you need to go to the dealer everytime you change something related to it. If someone wants to steal your car, it's not the immo that will avoid that.
But for your awnser, ask someone to recode the immo, it's just the opposite way of defeating it. I can't awnser completely your 2nd question but it should'nt affect the tune at all since immo and flash are two different things in ecu architecture