@jonathankampia Update: running the voxl2_io driver command modified to px4-qshell voxl2_io start -p 7 worked! The voxl-px4-start script correctly noted that all qshell commands needed to be prefixed this way, but for some reason starting the driver from there wasn't working. I just added the line manually to the extra commands section of the voxl-px4.conf file and it works now. Weird, though.
As for the second IO board we have, I am still confused why I can't update the firmware. Maybe the board is just bricked.