UPDATE:As of May 2022, Admin Tools 2.0 no longer supports the cloning operation.Backup My Org is now the recommended product to handle the migration of items, users, and groups from one organization to another. Please see the previous link for more information on the capabilities of this product.
As content and dependencies are cloned, Admin Tools prevents duplicates by looking for items in the target that share the same EXACT title and owner. If the tools find them, the cloning logic will attempt to wire the dependencies to it.
While this is necessary for the cloning operation's logic (to prevent moving a layer or map repeatedly, if it is referenced by multiple parent items), it is also intended to save time.
Moving larger services in small groups BEFORE moving webmaps that rely on the services can also save time.