You should back up both the Controller and Controller certificates.
Controller Backups
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When all of the ADS services and components are installed on the same server, and Microsoft SQL Server Desktop Engine (Windows) is used for the Controller database, you should perform a full backup of the server.
When the ADS services are installed on more than one server, or when SQL Server is hosting the Controller database, you must perform a custom backup of ADS.
Controller Certificate Backups
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Maintaining a secure copy of the Controller certificates is also advised. While a full system backup will contain the registry and the necessary ADS certificate entries, it is a wise precaution to also back up the ADS Root certificate and the ADS Data certificate by exporting them separately to files and keeping them in a secure location.
IMPORTANT
If you have neither a full system backup nor backup certificates, you will have to recreate your ADS configuration as with a first-time installation.