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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.

but rio is much more than the bitfile generation, it creates the interfaces and linuxcnc configuration.

it would be nice to have a visual editor in rio-setup like the vivado block designer