To be clear, there's the "calibration data" which is the result of the unit's self-cal routines, and then there's the "correction constants" which is the characterization of the attenuator, reference oscillator, etc. that's performed using external equipment.? Both sets of numbers are stored in the battery backed SRAM.
The calibration data is regenerated when the self-cal is run, but without accurate correction constants the unit will not meet its specifications.? If you're battery was dead when you received the unit, you've unfortunately lost your correction constants.? But if you're saying the attenuator was already in need of replacement, you would need to regenerate the correction constants anyway.
Regenerating the correction constants is covered in Section 2 of the Assembly-Level repair manual.
The supercap was probably ok.? It's only there to keep the SRAM running for a few hours while you change the battery.
-mark