In early September we had a hen hatch out 5 chicks they are doing great!
So about 6 to 7 weeks old.
They currently reside with the main flock but I don’t let the mom and babies free range (mostly cuz I don’t want anything to happen to them and I’m scared they won’t come back)
I can't argue about the predator risk. That is something we all have to come to terms with on our own. I'll not criticize you for your decision.
If they are used to sleeping in one spot they typically very strongly want to return to that spot to sleep. You do not get guarantees with living animals, practically anything can happen. I would not be concerned that they wouldn't return if they can, no fences in the way.
I’m assuming it’s not recommended to keep any hens in the same flock as their father ?! But maybe that’s not as big of an issue as I’m making it?
It's usually not that big of an issue, at least for the first few generations. There can be a couple of issues. If your flock (the rooster or the hens) have genetics that can cause problems then if you inbreed them that problem will come to the forefront if you breed related birds. For example, if you breed a cross-beaked chicken or one with crooked toes then that defect can become common in your flock. So try to not breed chickens with deformities. You should not breed those anyway but the problem can become a lot worse quickly if you breed related birds that have those genetics. For the majority of us that will not be an issue, our birds don't have those genetics anyway. But it is something to be aware of.
The other issue is loss of genetic diversity. If you inbreed chickens for several generations they can lose resistance to certain diseases, they are less thrifty (production and health), or they can have reduced fertility. How many generations this takes depends on things like how many hens and/or roosters you have and how random you are about keeping certain chicks.
There are different techniques to manage this. Hatcheries often use the pen breeding method where they might keep 20 roosters in with 200 hens so breeding is random. They can sometimes go decades without inbreeding issues.
Breeders often use line breeding (mating chickens to their offspring such as father to daughter or mother to son) to develop show quality chickens. This is the opposite of genetic diversity, they want to concentrate certain traits and eliminate others to get show quality chickens. But once they achieve the quality they want they switch to other techniques, like spiral breeding, to maintain as much genetic diversity as they can for the health and fertility issues. A good breeder that knows what they are doing can go many many years without having to bring in new blood.
Dad had a flock of one rooster and 25 to 30 hens. He went about five generations of inbreeding before he brought in a new rooster. I only remember him doing that twice when I was growing up. He'd get a dozen chicks from the feed store and use one of those cockerels to replace his current rooster.
I know that is a long answer but breeding parents to offspring or siblings to siblings isn't usually that big of a deal.
Also if they should be separated at what age?
Separated from whom? I let my broody hens raise their chicks with the flock. She handles integration so that when she weans her chicks they can make their own way with the flock. I've had broody hens wean their chicks at three weeks, some not until almost three months of age. But I have a lot of room so they don't have to be close together. If your coop or run are small it could be a problem.
If you are talking about separating the chicks from their mother, I leave mine with the broody until she decides to wean them. As I said, that can be anywhere from 3 weeks to 3 months. At 6 or 7 weeks of age they don't need the mother for food or heat anyway so you can separate them if you wish. With you keeping them separated from the flock you may have to handle integration yourself even if you leave them with her and separate from the flock.
What do you think you gain if you separate them?
