Removing CMOS Battery
Removing CMOS Battery
You're right, the GPU could handle the CMOS battery, so you don't have to remove the board from the case.
If you notice it, simply remove it. The issue arises because certain batteries are positioned inside PCI slots. Make sure the power supply is switched off to avoid problems.
Several boards include a collection of pins for resetting CMOS. Simply connect the pins lightly with a screwdriver. Your device guide should list where these pins are positioned.