I wouldn't recommend disabling any codes for the neutral position switch. There are some ECU calculations that are based on knowing whether the car is in gear or not. Disabling that code could throw off those calculations. It would be best to resolve the problem so that the code no longer is thrown. Hopefully it is just the sensor itself.
If you contact the shop that did the original APv1 tune, they should be able to combine your base map and realtime map (assuming you had separate base and realtime maps) and resave them into an APv2 format. If they are not willing to work with you or are no longer available, contact us and we can see what we can do for you. You can find out more information about the trade in program here
if you are interested.