You can definitely clean out a nest box after the fledglings leave. NestWatch suggests cleaning out nest boxes or birdhouses at the end of the breeding season. This isn’t absolutely necessary; often birds will clean it out themselves, but you can lend them a helping hand.
For nests that aren’t in nest boxes (such as in trees or bushes), there’s no need to do any cleanup. Why not? Most birds don’t reuse their old nests, no matter how clean they are. They typically build a new nest in a new location for each clutch. This reduces the prevalence of nest parasites such as mites and lice, too. Building a new nest in a new location also means predators are less likely to find the nest site before the young birds fledge.
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