You should be fine. If the controller with the faulty motherboard has already been taken over, you can power it down, replace the motherboard, and power up without affecting anything. Depending on your environment, you may need to schedule downtime for the giveback - if you're using CIFS, for example.
I have done this once on a V3020 cluster. Usually after a boot of a taken-over controller, it comes up to "waiting for giveback" - I don't recall if, after the MB replacement, I had to do anything special to get this to happen. I think on boot it detects that the partner is in takeover mode and knows not to boot - can anyone comment?
I would advise making sure all the eeprom settings are the same on the new MB. On the old controller (prior to the replacement), drop to the eeprom level, type printenv, and capture the output. Once the new MB is installed, do the same, compare the settings, and change anything on the new MB that doesn't match the old MB (change with setenv).
Sorry, without a system in front of me I also can't recall how to get to the eeprom - ctrl-C at boot, then service mode, or special mode, or something, then bye...might be different on N-series anyway.