Depends on how badly and why it flooded.
First and foremost CUT OFF any electricity to the chicken coop until it is thoroughly dried and wiring and all connections that got wet or MAY HAVE gotten wet are inspected and replaced, as needed.
Do you have batting insulation in the walls of your coop (like household insulation)? If so, this will probably need to be torn out and replaced.
What was the source of the water? Was it "clean" flood water (rain that pooled in low spots on your property and came over the floor level) or potentially vile & polluted (river water downstream from a city that discharges sewers into the water)?
1. If clean water -- remove all bedding. Let the coop air out as much as possible. Clean thoroughly while at it. So long as it's not soggy, chickens will probably be fine staying inside once the water goes down. Do not replace bedding until the wood is bone dry. You might consider some of the "stall dry" material but I'm not sure how that would affect birds who might eat it. Anyone?
2. If polluted water, then I'd try to remove the birds completely and sanitize thoroughly. Sanitize as if you were killing off poultry diseases. Perhaps apply fresh paint once things are dry.
Ed. to add:
If potentially polluted, or if mold is present, then wear protective gear -- respirator, rubber boots, etc.