It depends on how hard they look. I think the accepted wisdom on it is that normal servicing and diagnostics will not pick it up. So when you go in and have your service done or some other fault fixed it will not be noticed.
However if your engine melted and the dealer was suspicious then he could send the ECU to Germany for analysis and then it would be uncovered that it had been mapped.
So, on the whole it is very unlikely that it would ever be picked up that the car had been tampered with, but not impossible. It all depends whether you are prepared to take that small risk.
I will be considering having my 535d remapped when it arrives.
There is an obvious solution though, why not buy a 535d and then you'll have an extra 50 BHP direct from BMW. It may cost more but don't forget the new diesel ECUs are difficult to crack and so only a few companies will be able to do it for now and they will charge quite a lot.