They are either hibernating or have gone to their wintering grounds here in Maine. I'm assuming our chimney is a full time bat house because we have a lot of bats in the summer around here.
I have two flues and there's bat droppings only in the bottom of the one flue. My house is... complicated, I guess, but there's 3 levels: underground basement/garage, kitchen/living/dining and then bedrooms all the way upstairs. There's a wood stove and our oil burning furnace in the basement, hooked up to the chimney, not sure which flue(s). Then in the living room there's a wood stove and the kitchen has a pellet stove (again not sure which is on what flue). In those fireplace areas there's an ash pan thingie (I think) that goes all the way to the basement to collect ash (again I think that's what it's for). Last night we had fires going on the pellet and wood stoves on the first floor (this is usual for us in winter). Under the pellet stove in the ash thing is where the bats were last night. So they were below the level we were burning at. We only use the wood stove in the basement if we lose power (I think that's how we can get away with only 2 flues for the multitude of things hooked up to them) and again I'm unsure which flue it is hooked up to. I certainly don't want to kill the bats with smoke/heat but I suspect the bats are in only one flue because of the sporadic use of the stove in the basement.
A couple years ago I found a very dried and very dead bat in one of my lights in the living room. I'm guessing this has been going on for some time now.