I made the error of clicking the encoder instead of pushing PTT when trying to zerobeat WWV while having that high pitched tone come in, I found that the BFO got a saved shift point up +2kHz.
I ended up sitting down a few weeks ago and working out steps since it didn't always get saved.
Tune to WWV on the dial
Turn setup on
Reenter menu turn to and select calibrate
Zerobeat the WWV carrier. (May be difficult if BFO is too far off.)
Click encoder, select set BFO.
Zero the sideband off WWV. (My BFO frequencies were 11.997.0 and 11.995.0 for each sideband it's been 3 weeks)
Click PTT to set.
Click encoder, turn setup off.
Wait more than 10 seconds to ensure setting are saved before removing power.
Due to local noise I made a few attempts to set it correctly on a local AM station. Usually I set the sideband side wrong, so I had to go in change the BFO again. Due to rushing myself, I'd click "Calibrate" instead of "Set BFO" screwing me up to start all over again.
I need to go look at the code to see if the calibrate function just adjusts the ppm of the Si5351 or does something else. Either way, I got put off working on my uBitx until I figured the calibration routine out.