This is a bit of guesswork, as I don't have a dual GPU machine to test with - but this works across even different computers using the same screen.
The difficulty may be in persuading the system to swap profiles at the same time as it swaps GPUs.
The way to do this accurately would be with a hardware colorimeter, designed to test & balance the screen, then save a new custom profile.
The 'quick test' to see if that would be worthwhile & if the profile swap can be automated, would be to attempt to manually colour balance for each card & test if the profile swap can be done - either automatically or at least manually without too much effort.
You can use gfxCardStatus to force the GPUs to switch for testing.
Then use System Prefs > Displays > Color > Calibrate... & attempt to manually calibrate for each card.
If you can get it close enough to match each GPU manually, then all you need is to check the switching mechanism - whether the system will switch over automatically with the GPU.
If the switchover is automatic, or even an acceptable manual switch, but you cannot get the 2 GPUs to match closely enough by eye, then the hardware colorimeter would be the only way to get closer.
They are not cheap - entry level would be 80 - 100 bucks for something like a ColorMunki Smile, next up would be something like the Spyder
[If you're Googling for colorimeters, don't get the HueyPro, it no longer works with Yosemite.]