After taking my extruder apart for cleaning I found that the printer thinks it needs to raise to 5.85. When I calibrate my self with a sheet of paper I end up with -2.15. This is a value that the firmware doesn’t save for some reason.
Running the PROBE_CALIBRATION command will always start at Z=curpos + 5, where curpos is where the probe sensor detected the bed, which is ~2.3mm above the bed on my machine. When you set the correct Z offset and save, that should save an auto-generated config section to the end of your printer.cfg file which has a section for the Z offset that looks something like:
#*# [probe]
#*# z_offset = 2.395
As long as this value is saved to your config file when klipper starts up, then it will take the sensor position and subtract that offset amount from it to get the Z=0 position for the printer. If you want to make sure, after doing a G28 to home all axes, do a G1 Z0 F600 to move to the zero position, and use the paper test to make sure you’re getting just enough resistance from the nozzle (i.e. paper still moves, but has difficulty pushing toward the nozzle, might even bend instead of moving). If not, there are fine-tuning tools in Fluidd/Mainsail to babystep the Z offset without running the PROBE_CALIBRATE command, and which can save the modified offset to the config file when you’ve got it just right. In Fluidd it looks like this: