Under Federal law, you only lose the warranty to the extent the supercharger affects the component that fails. I am not aware of anyone with a stock Paxton kit installation that has had any failure of any kind when the kit has been installed by a competent installer like Mark Jorgensen and his Viper techs at Woodhouse. Furthermore, Mark and Woodhouse are a Five Star Dodge dealer and stand behind their work 100%. Also, the Paxton kit comes with its own three year limited warranty. Unless the '06 is new or is on an extended warranty, it would only have about one year left on the warranty anyway. I have had my Paxton on the car since it was new in May, 2006. I now have 13,000 miles on the car. The only problem I have had with the car is replacing the driver's side window regulator twice. And that is not related to the supercharger and is not unique to Vipers. If you want to track the Paxtonized car, you will need the DC reflash, 170 degree thermostat and a slightly colder plug. Good luck whatever you decide.
As for getting the mod investment back on resale, I agree with 1BADGTS. You will get something but not as much as you might want. But, people have had pretty good luck removing the mods; restoring the car to stock and selling both separately.