You don’t mention which edition you’re on. The Enterprise Edition includes the ability to export a project from one instance and import it into another. Sorry, I don’t remember any more what version that starts in, but I know it’s present in 6.7. So you might want to upgrade both instances to 6.7, and then consolidate.
And BTW, other than project export/import, there’s no way to consolidate multiple instances. You would just have to pick one of them and perhaps try to recreate the history of the projects from the other instance using
sonar.projectDate. Note that this is tedious and error-prone, and you can’t do it retroactively or backwards. Your first analysis of a project has to be with the oldest date you want included in your history.