Yup, I mark deflocks, rehairs, repaints, or anything that's been touched up. DF, RH, RP, etc. Although most of mine are pretty obvious since I give them different hair colors, but I don't want someone someday to try and sell something I've rehaired as an OMG SO RARE VARIANT.
You may think that it's obvious that your pony has been restored in some way, but a lot of people think that ponies with different hair or a switched tail or anything like that is automatically a rare variant or something rather than a customized pony. Or even if they know better, they'll try and sell it that way anyway. So you should always mark them in some way that cannot be removed by a reseller.