In my experience I have always been up front with the dealers about remaps.
When we had the 307 we had a problem with the FAP that had to be replaced under warranty. The service manager at the dealers said that the remap may well have contributed towards its premature failure, but would keep quite about it as far as getting the claim authorised with Peugeot. A job's a job to him, so why rock the boat?
Sent from my ipad 5 demo edition