Unfortunately there wouldn't be a way to combine the two databases. If you have some different machine groups in one of the consoles that you want to keep you could export the machine groups and import them to the console with the database you want to keep. This Protect Help article shows information about the import/export function for machine groups: http://www.shavlik.com/onlinehelp/Protect90HTMLHelp/Machine_Group_Dialog__Top_Section.htm
Basically you'll want to choose which database to continue using and upgrade. Then follow the steps in this document to migrate the database: Moving a Protect database from one SQL server to another. Once the database is migrated you can run the version 9 installer, and it will upgrade the database for Protect version 9.
I hope that helps. Let me know if you have additional questions!
Oh, and make sure to do a backup prior to the upgrade!
Just in case
Adamg23, the migration tool found here: http://www.shavlik.com/downloads/mtg-prt-9-0.pdf says that it will migrate the following data in the box below. However, the doc also states that it will overwrite whatever exists in the database so I won't be able to use it in my situation. In reference to your export/import machine groups comment above, how do I get all this other data migrated and selectively merged into the primary server?
What is migrated by the Migration Tool?
• Agent policies
• Background tasks
• Custom patch XML files
• Custom PowerShell scripts that have been imported into the database
• Database (local only)
• Distribution servers (remote only)
• Files referenced by the Machine Grouplink to file feature
• Groups (machine, patch, service packs)
• License activation in a non-proxied online environment
• Global and user settings defined on theTools > Options dialog
• Patch store if contained on a local drive (up to 10 GB of data and data that is not more than 90 days old)
• Results (scan results, deployment results, etc.)
• Scheduled tasks for the Shavlik Scheduler (the Microsoft Scheduler is not supported by the Migration Tool)
• Some user-specific options
The migration tool won't really assist in being able to selectively merge data from one console/database to another. That's not what it was designed to do, and unfortunately we don't currently have a tool that will allow you to selectively move/merge data like what it seems you're looking for.
Currently the options are basically you move everything (no merge), or export/import machine groups - machine groups are currently the only piece of Protect that have the export/import option.
If you would like us to look into creating more functionality around exporting/importing I would recommend submitting a request at http://shavlik.featureidea.com so that our product management team is aware of this.