I believe from chatting with Chris @ VAP if the dealership has updated your ECU while in for service, when you come to reapply your tune, the box will alert you that the checksums don't match. At this point you can pull your stock again and send it over to them for an update.

 

I always revert back to the OEM Tune when I take it in for service just to ensure that they don’t brick the ECU with an unannounced update.

 

If I had a tune *cough* that would be exactly the thing I would do too...