I am at the point where this Navio2 thing is going in the garbage and switching to Pixhawk or the cube. Everything was working fine. untill now
If emlidtool rcio check was OK last day and broken now, you have a problem.
On my side I run the same commands “sudo emlidtool ardupilot” after stopping Ardupilot and rcio is fine.
Can you check the seating of the Navio on the raspberry. Pins are to be fully plugged and all four screw tight.
Reformatted and everything ok now.
Just a note. That happened after I assigend an RC function to RCOUT 13. Not sure if this was the cause but will do it again and see if the results are the same.