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You will need a custom mcode that calls an executable script that uses 'halcmd' to set the appropriate hal pins.

Here is an example that does this but for different hal pins so you will need to modify to meet your needs:
forum.linuxcnc.org/21-axis/53531-change-the-axis-limit#307778

Yeah I didn't remember that right. Then I wonder if that's the problem here.