Well at 9000 miles (only on 14k now) I had a new gearbox fitted as there was a loud vibrating rattling noise when rolling in gear and not accelerating. Secondary lay shaft they said it was.
If that gearbox died because of the remap I'll never know. I hardly use my car as it is and I rarely rag it hard. But i had a remap on my previous car a DS3 for 4 years and had no problem.
Some people say main dealer can tell if the car has been mapped but I've never been caught out and to be honest I doubt you'll get caught. When I had my gearbox changed tho I did have the map removed then put back on after it was fixed. My 308 has been in a few times for various little things and they never said a word.
Always ask them tho if they have done a edu wipe or flash. As it will reset to factory ECU setting and you'll need to get your map back on.