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I breed father/daughter/, mother/son, cousin/cousin, etc. I don't see too many problems. Wolf teeth every now and then but nothing that can't be bred out of the line. Half brother to half sister is a safe breeding. As long as you breed the offspring to something that is semi related to them. Or not related to them. I wouldn't even try breeding brother to sister. Its a big nono to do, unless you have a lot of experience with genetics. Most rabbits breeders won't even attempt it.
Its possible there was something wrong with your breeding line to begin with. That could be why you saw some probems with them. Best thing to do when they show up like that is to breed them out by breeding down with the healthiest rabbits of the litter. Or outbreeding to another line. then start linebreeding them again.