I see a couple of options.
First, you can set a different edid file for different monitors. The proprietary Nvidia driver allows that. The syntax is something like:
DPF-0 and DFP-1 are the naming convention the Nvidia driver uses and it may change depending on the interface (VGA, HDMI, etc). Check your '/var/log/Xorg.0.log' to get the proper names.
Option "CustomEDID" "DFP-0:/etc/X11/right.bin"
Option "CustomEDID" "DFP-1:/etc/X11/left.bin"
The Nvidia driver also saves part of your customization on your home directory (in ~/.nvidia-settings-rc). That is the reason why most settings you save on the 'Nvidia X Server Settings' are correctly loaded every time you log into the desktop (without saving the info on /etc/X11/xorg.conf)
The latter works because there's a script set on 'Startup Applications' that load the configuration from your directory. The content of the script is very simple:
I imagine that if you save your setting using 'Nvidia X Server Settings' (or nvidia-settings), you can reload them by running the script manually again.
sh -c '/usr/bin/nvidia-settings --load-config-only'
Hope that helps. Let us know if you need more help with that.