You will have to calibrate the whole section for the cal constants to be stored in the EEPROM. Per the note on page 54 of the Cal Procedure,
"Caution If you skip any of the steps within a section of the adjustment procedures, the niDMM Close External Cal VI and the niDMM_ExtCalClose function do not allow you to store your new calibration coefficients. Instead, NI-DMM restores the original coefficients to the EEPROM."
However, performing the sections: Adjusting Linearization and Adjusting DC Voltage in their entirety will allow you to have updated calibration performed on DC Voltage measurements with a new cal date stored to EEPROM.
National Instruments Precision DC Hardware Engineer