If you’re using 2.0 it always tries to sync the latest changes so changing something only in rekordbox (don’t forget to re-export the XML) would cause the changes to be synced over. Also make sure you’re not protecting one of the databases you are trying to update (in the preferences).
If you want complete control over this (a lot of people do), I would suggest hoping over to the 2.1beta which lets you decide where to import from and where to export to. That way you can be sure that you can fine tune what is synced in what direction.
An upcoming 2.1beta build should give you even more fine-grained control over this.