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Bird boxes

I wonder whether anyone can give me some advice; Last year our nest boxes were very busy, blue tits made good use of some of our boxes and the tree sparrows set up home in our nice new nesting box for the first time, they successfully reared 4 broods.  Every time I though of clearing out the box, there were more babies there chirping merrily!  The boxes haven't been cleaned out yet, and now are being used at night by roosting birds so I don't like to clear them out as I might discourage them and would be removing their insulation.  What is the best thing to do?  I want to provide a safe place for the birds to roost over winter and allow them to nest in the spring.  If I leave the cleaning too late they might be suspicious and not use the boxes.