You can do it this way:
- configure new global dedupe storage policy using your new S3 bucket and MA
- configure new secondary copies in your existing storage policies pointing to your new S3 dedupe storage
- run aux-copy
- disable backup activity and promote S3 secondary copies as primary copies
- re-enable backup activity
- delete you old copies from storage policies
Using these steps your storage policy copies will honour 512KB block insted of 128KB.
Index will be rebuilt directly from backup data.