if an aftermarket supercharger then the remapping is referring to the new SC map, if its one of mine then the data logger ought to still work, if it doesn't, i'd certainly like to know about it
but yeah you're basically in the hands of the dealer with a car with a 3rd party SC, at least for any parts that can be blamed on it, ie if the roof came off the sc couldn't have cause it, so it ought to be warrantied, it'll depend on whats left of the factory warranty, and how the dealer is positioning it.
the other reason is that lotus issues updates for the cars, so far its been two or three for the lifetime of the car, thats the other reason, the one thats not to worry about.