It's good practice to create a backup before making changes, particularly in a production environment. If you don't have one, I suggest making a backup of the current state before making further changes.
Typically, unregistering a datastore through Server Manager also unregisters it on the ArcGIS Data Store. Sometimes this may fail if there's a connectivity issue between the Hosting Server and Datastore (or other reasons). In such cases, you can manually run the unregisterdatastore utility on the relational datastore. Note that an unregistered relational datastore doesn't mean data gets wiped; it's simply in a state where the underlying postgres database isn't running.
The registerdatastore and configuredatastore utilities won't create a new database if one already exists. As long as the configuration files at \arcgisdatastore\etc are intact, either of these tools can be used to reconnect the existing relational database to the Hosting Server site.
For the most part, you can think of the registerdatastore and configuredatastore tools as providing your ArcGIS Server access with a database connection file containing credentials and other database details without altering the database itself.
If you encounter errors about an existing datastore during re-registration, you may need to modify the dsconnections.lst file on the Hosting Server. Various technical articles cover this workflow such as:
Let's hope the initial issue was just a momentary blip that caused the ArcGIS relational datastore to fail to unregister itself. Otherwise, it could be a sign of deeper issues to come.
