Your only option is to manually copy the scripts/apps/prompts/skills/CSQs/teams/resource groups/etc. There is no documented process to merge the databases and all of the historical reporting data sadly.
As Jonathan says, you'll need to merge the config manually.
The Historical data will be a problem - you won't be able to merge that into a single new cluster.
Find out if historical data is important to the customer. It might not be, or they may be willing to lose the data from one clsuter. If that's the case you can use the upgrade tool to upgrade the clsuter that has the important HR data, and then merge the config in from the other system.
If they need to keep the data from both, then you have a few options:
1) Change the plan and maintain two seperate clusters, each upgraded with the upgrade tool.
2) Export the data from one or both clusters to a seperate database server. You would then need to come up with some way of reporting on that data....
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