For Quick Base to Quick Base Syncs since the Sync function is able to read what you have set as the key field in your source table you are correct that there is not a way to change the refresh key. It is designed to stick with the source key. I have seen some users with use cases like yours where an alternative refresh key would be helpful on a Quick Base to Quick Base Sync it just isn't a functionality in place currently.
As I often suggest in this instance I would encourage you though to include that feedback in our User Voice as an enhancement you would like to see for Sync. UserVoice is our Feedback Platform- which can most easily be accessed from the My Apps page in Quick Base by clicking on the orange Feedback tab that appears on the left hand side of the page or at
http://quickbase.uservoice.com . This forum is used by our development team to explore customer suggestions for enhancements / changes to the platform. Our Automation Team is always interested in hearing what functionality users would like to see in our features like Sync as we plan for future development. I'm sorry there isn't a native functionality I could suggest in this instance.
