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Scrape it and use a spray to control pests . Then put in clean bedding and add in the birds again...:frow

Well that's all good for you but the OP said this is an old Coop so possibly the wood will hold moisture before it drys completely and mold will grow...:frow

If it doesn't completely dry then mold spores grow fast and you will have another issue on your hands..

That would soak everything and then take way too long to dry out..

Most things are gone unless mereks was in the flock? Just scrap it down and spray with pertharin spray. I wouldn't be too concerned though. Then add in pine shavings and begin putting in the Birds..