First off, is your dog neutered? My doberman pinscher isn't and he'll mark up a storm if he goes into my mother-in-laws house or my gma's house because they have pets that are older and have marked all over the place, even though they have done everything but replace the carpet. Your dog IS house trained, he just wants to mark where she's marked, it's a territorial thing and I would clean the carpet a few times and use some special pet-scent removal spray to see if that'll work. If not, I'm sorry to say, you may have to replace the carpet.
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