@Phaedrux Wow this is working! I added this before the Z homing lines and everything work properly.
I also added the switch back to initial mapping at the end (so I don't do this trick to the homey.g also)
; homeall.g ; called to home all axes ; G91 ; relative positioning G1 H2 Z5 F6000 ; lift Z relative to current position G1 H1 X-480 Y-480 F3000 ; move quickly to X and Y axis endstops and stop there (first pass) G1 H2 X5 Y5 F6000 ; go back a few mm G1 H1 X-480 Y-480 F360 ; move slowly to X and Y axis endstops once more (second pass) G90 G0 X-40 Y5 G91 M574 Y1 S1 P"nil" M574 Z1 S1 P"ystop+e1stop" G1 H1 Z-405 F360 ; move Z down stopping at the endstop G90 ; absolute positioning G92 Z-2.4 ; Adjust Z offset G1 Z20 M574 Z1 S1 P"nil" M574 Y1 S1 P"ystop+e1stop"
Thank you Jay and Phaedrux for your help.