Try PROBE_CALIBRATE in the Console. Use a piece of paper, it should fit between nozzle and bed, you should be able to move it with slight resistance. Save it with SAVE_CONFIG.
This. Checkout the Klipper documentation at https://www.klipper3d.org/Probe_Calibrate.html#calibrating-probe-z-offset
Not sure if it’s available on klipper, but try sending this:
M211 s0
This is the marlin gcode for turning off the software endstops which prevent you from going negative. (You turn it back on with S1 for normal printing.)
To calibrate z offset, set it to zero, home z, then move the nozzle to where you probed, read the nozzles position (mine is about -2.5) and set that as your offset.
You can check status of the software endstops by sending just m211.. if it’s in klipper it should return something.
If it’s not in klipper there should be something similar.
Have you got a "zero_reference_position" under [bed_mesh] settings?
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