Do you have him close to any other rabbits? We had a doe who started spraying when we put her next to a buck. As soon as we switched out the buck for another doe, she stopped.
I have an intact male and two intact females. When the male could be close to the females cage he started spraying although he had never done so until after getting the females.
I put an Xpen up to separate the bun room. As soon as the male could no longer get close to the females cage he stopped spraying.
He's male and he's hormonal, that she is his sister or has babies and is nursing doesn't really matter. If he was ever with her he would still probably breed with her. But since they have always been near each other, moving one of them might be upsetting to them, so that is something to consider. Maybe having the babies around is riling him up too.