This is on Arch Linux. After an update, my 2nd monitor was no longer detected. I downgraded nouveau to the Arch package version 1.0.15-2 (from 1.0.15-3) and the problem went away. I also had to downgrade xorg-server due to dependency issues, so it's possible the problem could be there and not in nouveau itself. My xorg-server package is now xorg-server-1.19.6+13+gd0d1a694f-2, down from xorg-server-1.20.0-2.
Both monitors work fine in the downgraded configuration, but only one works with the latest updates.
When things weren't working, /var/log/Xorg.0.log showed the message "failed to find screen to remove" for one of the GPUs. This is no longer the case after the downgrade.
This might be the same problem: https://bugs.freedesktop.org/show_bug.cgi?id=106586
It might be the same problem, yes. It definitely looks similar.