Recently I had to reinstall an SCCM 2012 R2 instance, and came across a strange error when I ran the Prerequisite Check.
Dedicated SQL Server instance: Configuration Manager requires a dedicated SQL Server instance to host the site database. You selected the SQL Server instance that site hosts the Configuration Manager database for another site. Select a different SQL Server instance for this new site to use, or resolve the conflict by uninstalling The Other excellant site or moving to a different database SQL Server instance.
After some research it turns out this (in my case anyways) is due to the SCCM uninstall process not properly completing. SCCM doesn’t need it’s own SQL instance, it just requires that you only have one SCCM instance per SQL instance. To make sure this is the case, the prerequisite checker looks for a few registry keys on the SQL server that the install is looking to use. To fix this error, delete the following keys from the SQL server.
After they are deleted, run the prerequisite checker again and viola!
I hope this makes your day at least a little bit easier.