Hi Enno,
you can use the "synchronize storage" operation to copy all files from one storage to another.
After that you can use the "cleanup storage" operation to delete all files that have at least one other location from the selected storage.
Since synchronize storage made sure all files are on at least one other storage all files can and will be deleted from the selected storage (S3).
After the successful run of the cleanup storage operation you can delete the storage.
Best regards
Nicolai