Update: It is fairly easy to change the Empire owning a colony, at least if you start fresh and you manipulate the Sol system at start. A single edit in the appropriate table (Population) of the RaceID field, and you are good
So just plop empty colonies in the solar system, then go to the table, and change RaceID. You can also change the population while you are at it. If you want to go into the details, then you can edit installations with the aptly named table PopulationInstallations.
When play with database I always recommend/follow this simple rules:
1- have a dummy database for testing, your current campaign will do, the more data the better, but remove all other save from the database
2- 1 database per save - easier to work with
3- backup always before start modifying
4- before making a change try it first on the dummy database