Neuspeed re-flash negate factory updates?
 

I had the Neuspeed re-flash done not long after I purchased my A3. After reading some posts in here about factory ECU upgrades, I was wondering if having a 3rd party chip negates the ability to receive any factory updates. Do I even want these factory updates? I know I can have Neuspeed bring my system back to stock before I go to the dealer, but even if I receive factory upgrades, I'm assuming they be lost when Neuspeed re-flashes my car after the service.