Yeah I have learn't they can't detect the actual re-map but can see how many times the memory has been 'flashed' so if it was installed or not they would still be able to see you had re-mapped at some point. Not sure they would check it as routine, wouldn't have thought so, I don't have mine serviced at a dealer anyway, get it done at a local VW/Audi specialist, just take it in for any recalls/warranty work.
It depends on how much you value your warranty against modding your motor, personally I will sell my ED30 at 3 years old so would never have the chance to re-map if I wanted to keep my warranty for the duration!
There was one chap on here who had his dealer re-map his motor, was more expensive (£800) but kept his warranty - can't remember what re-map it was though.
I am loving my Bluefin ED30! But if you read the main thread u'll see its got its critics!