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I didn't know lime was used to control mites. I use food grade DE, or if it's really bad, ivermectin, the 1% injectable, in their water. 4cc (or ml, same thing) per gallon.
Mites don't fly, though, so it sound like you have something else. Yes, insects can come in on hay. Flying insects wouldn't be an infestation on the birds. Just near the birds. I'd try to get hold of one of the insects to find out what it is, and see if it's something you need to get rid of, or if it's just a bug the girls will chase around, catch and eat when they can. I have a little banty hen that used to sway back and forth, staring straight up, watching for mosquitoes. When she saw one, she'd leap up and catch it. All the chicks she raised learned to do that, too.
Why did you put them indoors? Are you in an extremely cold area? Like sub-zero a lot? Many people keep chickens in extremely cold places, with just enough heat at night to avoid frostbite.
Is this your first year to keep chickens? I don't have any idea what your warm weather arrangements are, or how much space you have, or what your climate's like, but moving them totally indoors just seems really odd to me.
ETA:I meant to say had a little banty hen, that was a long time ago!