As content and dependencies are cloned, Admin Tools prevents duplicates by looking for items in the target that share the same title and owner. If the tools find them, the cloning logic will attempt to wire the dependencies to it.
While this both necessary for the cloning operation, and is intended to save time, this same logic should be taken into consideration when moving content to a target that has pre-existing items prior to cloning.
Note
If you want to save time by manually standing up your feature services or map services, the cloning logic will allow for this.
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