That ammonia smell in the coop might be a silent killer, hear me out

I was at the feed store last Tuesday picking up oyster shell and I overheard a lady talking to the clerk about how her hens seemed fine but she was losing a few every couple weeks. The clerk asked if she could smell that sharp ammonia punch when she opened the coop door. She said yeah but she figured it was just normal. Clerk said no, that smell is literally burning their lungs and it creeps up slow. I went home and stuck my face right in my own coop and nearly gagged. I had been airing it out but not deep cleaning the droppings board enough. I stripped it all down, put down fresh pine shavings, and added more ventilation near the roof. It's been 5 days and the difference is unreal. The birds are more active and eating better. Has anyone else had this happen without seeing obvious sick birds first?