Z axis issue after upgrade from stock FW to Marlin 2.0.7.2 on Ender 3 Pro
This seems like Z homing issue. Sounds pretty frustrating, so I will try to give some hints, though I do not have Ender 3. Also maybe my few questions will be helpful.
Did you &quot;adjusted all the wheels on the printer&quot; after the Z position was zeroed? This could be crucial, especially that firmware may raise Z up after homing (e.g. to 4mm). The G-Code you have sent makes simple Z moves: rises to 2mm, then lowers to 0.28 mm above the sea level (and F is denotion of speed). And obviously this should happen AFTER homing Z axis, not earlier - could you check earlier G-Code for G28 call?
If you can manually move the bed out of heatend's range (to avoid crashing it) then I suggest to use own file containing only two commands to experiment with Z homing only, e.g.:
G90             ; absolute positioning (just to be sure it is not incremental G91)
G28 Z           ; homing Z axis
G1 Z0.0 F100    ; firmware may have raised Z up slightly, so lower again to 0

If homing would cause the bed accident, than I am unfortunately right - or:
(Added after tracing real problem) Check if Z axis is not loose - e.g. coupler screws are tight - so Z axis cannot rotate on its own by gravity and wight of carrige. When Z steppers are enabled, you should not be possible to move carriage up and down with slight pressur of hands.
Does the printer react to Z endstop? This is first thing to check, actually. You can you press it with finger during Z homing to check if it would react properly (Z homing stopped).
If not, then... did you compile Marlin on your own? For example maybe the Z endstop is or should be inverted. More insight is needed then against the Configuration.h, e.g. file for Z_MIN_ENDSTOP settings. Would be good to have its version from previous firmware, or google some valid Ender 3 file to compare with.