When cloning a Registered Service, or RS, from one ArcGIS Organization to another, it will still point to the original source for the underlying data. Support sometimes gets questions about why this occurs, and this article provides an explanation.
What’s Happening and Why
A registered service is a pointer or reference to a set of data used to populate a map layer. That information may be in your ArcGIS Organization, or it may come from elsewhere. Since a RS is just a pointer, when you clone it, it will still point to the same reference. This is because, when performing operations in Backup My Org (BMO), you only have the ability to perform operations on content in your ArcGIS Organization. If you tried to clone a RS that pointed to a source outside your organization and its source, the operation would fail because you don't have permission to clone the source. Because there is a possibility a RS could rely on data from outside your ArcGIS Organization, Esri does not provide enough information about the registered service’s data source to clone it as well.
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Again, note that Esri does not provide enough information about Registered Services to determine if the table is in the appendix or another book. It treats every Registered Service as if the table is in another book. This is why, when you clone your RS from one ArcGIS Organization to another, it still points back to the original source - even if the service’s URL is in the first ArcGIS Organization.
Hopefully, this explanation helps you understand what's going on when Backup My Org clones a Registered Service.
How to Get Your Registered Services to Point at Your New ArcGIS Organization
The only way to get the data for a Registered Service from one environment to another is to republish it manually. Once you have done so, you can clone the items looking at the registered service from one ArcGIS Organization to another. During the Post-Processing steps in BMO, there will be an option to update the URLs for these services to look at the data from the new service you published.
If you have already cloned the items over, you also have the option to use the “Find / Replace Web Maps Services URLs” tool in Admin Tools for ArcGIS. Using this tool, you can update the services to look at the data in the destination ArcGIS Organization.