When I went to p/ex my Honda S2000 fitted with after-market sports exhaust Audi dealer wanted to be assured it would be exchanged with OE system re-fitted. I was questioned as to whether I had done anything else like messing with the intake system etc. It seems main dealers want clean standard well presented cars, not tarted up things that would stick out like sore thumbs on their smart forecourts.
Suited me fine as the cars p/ex value was not enhanced by sports exhaust so it was sold seperately as were the non-OE expensive luxury mats, VERY heavy non-OE gearknob and set spare smaller diameter winter wheels and tyres.