Generally, hosted services that are utilized by a web map or a web app will automatically be migrated and wired appropriately during a cloning operation. However, if services are registered to a different data source (such as a federated server or, for example a production environment), the item will migrate to the destination, but the URLs will still remain pointing to the original source, and the references will need to be updated to the new location where the services exist. Admin Tools does have the capability to perform this task with the "Update Items Content URL” tool:
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NOTE: For Web Maps, you may also need to employ the “Find and Replace Web Maps Services URLs” tool.
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