You should be okay. I had my manifold replaced last month and I didn't even change the tune to stock. When I made the appointment, I asked the service rep if it would be a problem since I had tuned the car and had a downpipe and she said it should be fine since its a common part to fail. And it wasn't a problem.
You may want to consider getting a carbon cleaning while they have the manifold off.
Taking the car in for the faulty manifold problem tmrw. Still covered by VW extended warranty and should I expect any grief over intake, exhaust, and a boost gauge installed ?
Sent from my iPhone using Tapatalk
If your boost gauge uses an adapter tapped into the manifold, I recommend removing it. I disconnected/removed my catch can and boost tap to ensure all connections to the intake manifold were stock before taking it to the dealer. Dealer did asked my if I was "modded" and my response was yeah...the intake and exhaust They warrantied my manifold...no issues.
Good luck
Left boost tap on, no problems. Did manifold, took care of the water pump while there, and did carbon cleaning. Runs great now.
Sent from my iPhone using Tapatalk