So basically there is nothing I can do?
No, that's definitely not the take away message there.

I just meant that if you choose to use serious chemicals which affect ALL life, not just the harmful things, then this should only be done under situations like a severe outbreak of an incredibly serious disease. 'Burn the barn to the ground' style pathogen management. It does have its place, is what I was trying to say there.
Your situation, though, I don't know well enough to advocate for or against such measures. What you should do depends on what your situation is; the soil, the animals, the disease or problem, and the amount of space and finances you have to work with all decide the issue for you.
If your soil is healthy enough now, you could try boosting its health so it gets into balance, full of beneficial microorganisms and fungi etc, which will then naturally control pathogens, odor, etc. Lime will help that.
If it's already unhealthy soil, and that unhealthiness is due to chemicals which linger for long periods, rather than just the soils' nutrients or 'beneficials to harmfuls' ratio being out of balance, then chemical treatment may be all you can continue to do with such a place. In this case concrete yards would be easier to maintain animals on. And in that case, chemical or very strong cleaners such as bleach or Oxine would be ideal, or tea tree oil. Probably the latter two specifically.
If you had a yard completely concreted over, or one with chemically treated and dead soil, then you'd really have a work on your hands to obtain and maintain full health in your chooks --- that said, most of us will never have 100% health, nor will our animals, and many of us can still have quite decently healthy birds on plain concrete floors. But when there is no healthy soil to keep bacteria, fungi etc in check, you either have to restore the soil, move the livestock, or resort to concreted floors and treating them chemically or otherwise unnaturally.
Personally I lack the knowledge at this point to try to tackle soil that's been Roundup-sprayed, bleached regularly, or contaminated with other serious and inorganic chemicals including artificial fertilizers. I'd just try to keep them off it. I am, in fact, currently having health issues with my animals because the place I recently moved to has had some seriously crazy applications of artificial fertilizers inflicted upon it for decades running. This inhibits uptake of some vital nutrients up to 100%. Which is, of course, a death sentence for animals kept upon such pastures. Sometimes keeping them on concrete or wire is healthier than on the ground, as much as it's unnatural and preferably to be avoided.
What your best health solution is depends on your situation. That's all I can really say there, sometimes trying to provide scenario-specific info is more confusing than helpful.
Best wishes.