Is there a way with the Phaserunner and/or CA V3 software interfaces to sync the difference

As measured at my Phaserunner battery input terminal by my in-calibration, 6.5 digit Keysight bench meter, my pack Voltage reads 49.0 and the Cycle analyst reads 48.7. Is there a way with the Phaserunner and/or CA V3 software interfaces to sync the difference?

No way to "sync" them, but the CA has some advanced settings that allow you to alter the voltage readout. I recommend noting what it was before changing it, in case your change doesn't work out.

I believe it is called "V/V"; in the calibration section. The Grin site or CA3 manual should have info on this.