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I think you might have to clean these up. Here is how to find the folders that did not get moved:
aws s3api list-objects \
--bucket test-bucket \
--query 'Contents[?ends_with(Key, `/`) && contains(Key, `b/`)].Key'
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Thanks. But that means I will need to recreate all the empty folders again at the target location. That might not be a good thing performance wise, in case the nested folders are deeper to many levels.