It would help to have pics of your set up.
I have a coop that is divided but both flocks can see each other so it would be hard for me. I suppose technically they are one flock but the Dels are seperate. One roo and his hens.
Now if you have two coops 100 feet apart that's a little better. Treat the sick flock and watch for signs of illness in the second. Make sure your healthy flock has the best nutrition you can give them and I would give them vitamins as a precaution. It Can't hurt but might help. The healthier your flock the less likely they will get sick. Make sure air flow from one coop to the other is blocked. This can be done with a "wall" of tarps or shrubbery. Make sure water and coop are as clean as possible. Of course it all depends on what the sick birds have.
A good bio security plan willl help. Change your clothes when going between coops. Don't wear the same shoes or wash them with a disinfectant. Don't let anyone who has birds come into your coop. Unless you trust them. Don't buy eggs from people you don't trust. Birds can be carriers. Quantine any sick birds immediately and have an infirmary for sick birds. Not if they get sick but when. Keep all wild birds away from your flock. Don't over feed scratch so that there is leftovers on the ground for vermin or wild birds.
Of course all of this may seem impossible but do your "best". No one can expect more than this. Chickens can be fragile and drop dead for unknown reasons. Seem perfectly fine in the morning and dead in the afternoon. One sick bird does not spell epidemic, two, three, four and you've got a problem.. Again the minute you see or suspect somethings wrong seperate the bird.
Hope this helps
Rancher