Do I need to calibrate my instruments separately when I upgrade from the 4200-SCS to a 4200A-SCS mainframe?

No; when the 4200A-MF-UP service is selected, the 4200-SCS is converted to the 4200A-SCS mainframe. This system gains the Clarius software.
All supported instrument modules in the original system will be moved to the new, 4200A-SCS mainframe and will receive a factory calibration with the system. Additional calibration is not required for instrument modules installed with the upgrade.