The computer absolutely WILL know the difference. The computer has access to the vehicle speed on the CANBUS and it internally knows it's own shaft speeds, input speeds, and output speeds. Vehicle speed will no longer correlate as expected with engine RPM, and with the CVT the transmission computer is designed to keep the engine in a specific RPM band and to use changes in the gearing for differences in road speed.
I would say it's unlikely that the computer will accept a change in gearing without throwing some codes at the very least. Since it's effectively impossible to know the programming of the TCU as this is proprietary closed source software the only way to know for sure would be to try it. Buy I would guess it probably won't work.
GD