That;s what I was getting at. They may be able to tell that you have altered the programming, it really depends on how hard the tech wants to look. Most likely they won't give a fuck anyway, especially if they're cool.if you purchased stock mode also, and switched to stock before going to the dealership, then it's going to be hard, but yes, vw can still find out that it was chipped, if they really wanted to.
Talk to the service writer at your dealership they are the ones that make the warranty decisions, be a nice guy and don't be shady about what your plans are for the car. There are some pretty heavily modded cars owned by employees at my dealership. I wouldn't let warranty stop you from doing shit to your car, but it's your call.