Thank you! I thought I had already tried that. But now that I have tested it again, I can confirm that it works if you only change the sign of calibration_lockin.accel.
This would be something that could be changed in the documentation. Maybe someone with access can change this section to something like:
Sometimes you would like the index search to only happen in a particular direction (the reverse of the default). Instead of swapping the motor leads, you can change the sign of <axis>.config.calibration_lockin.accel.