Geneticist friends have told me that you won't see any effects until after about 5 generations. Most of the deformities we see in CB clowns are from sub par conditions in the rearing tanks.
While I haven't bred siblings, it's pretty common to do so. I wouldn't worry too much about going a generation or two. If you get past that, pair up a juvenile with a fish from another breeder or (better yet) a wild caught fish.
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