If you're breeding your chickens in a controlled way, one thing you can consider is keeping a chicken who expresses an undesirable, recessive trait you're concerned about.
1). You can use this hen or rooster in test matings to determine if other chickens carry the trait. If the other bird is a carrier, some (theoretically 50%) of the offspring will express the trait (the rest will be carriers). If the other bird is free of the gene, none of the offspring will express the trait (but all will be carriers).
Once you have found a breeder free of the trait, you can proceed happily knowing that their genetic material is "safe".
2). If you're doing conservation breeding, remember that it's only "gene pair ww" which is the problem (in our example). All the chicken's other genes may be ok, and could contribute some valuable genetic diversity. To "suck" the good genetic material out of your problem chicken, mate it with a non-carrier, and then mate the children either with A. one another or with B. a non-carrier. 50% of the grandchildren from A, and 25% of the grandchildren from B, will be free of the problem. You can test by breeding back to the grandparent...
Yes, this approach will use up a lot of elapsed time (as birds grow to breeding age) and generate a lot of chicks, but it gives you a degree of certainty that you are breeding the trait out and not just breeding around it.
I have a couple of young Crevecours, both of whom are starting to show evidence of either wry tail or some kind of swelling of the oil gland causing them to tilt their tails voluntarily.
If it's wry tail, I think I've resigned myself to keeping them around and trying to breed from them anyway, as the breed's in such trouble.
Best - exop