You can check this and verify you have 2 entries.
http://www-10.lotus.com/ldd/stforum.nsf/DateAllFlatweb/728b8766ef25921285257984004db84f?OpenDocument
Make a backup of db2. Then you can delete the new one with the command:
remove from ssc.deployments where depid='xxx'
where the depid is what you saw for the entry of type "com.ibm.lotus.sametime.systemconsoleserver" and a OffVersion of 8.5.2.1 in the xml from the linked post. Then double check you're settings in console.properties and productConfig.properties and run the registerProduct.bat -upgrade again. If you're settings are right, it won't create a 2nd entry but will update the first.