What do you expect a floating pin does?
I expect it to read 0 volts. It's affecting my voltage divider into the adc because as I change the supply voltage, that pin voltage changes also. However, I am powering the chip through a 5 volt regulator so I don't understand why changing the board supply voltage would change that pin voltage (even though it should be zero). After removing the second channel from the SAR everything is working as it should and the pin now does read 0 V when left floating.
You are using ADC_CountsTo_Volts(). This API assumes the Vdda to be correctly specified (in .cydwr view, System tab). When changing the supply from 5V to 3.3V or back will affect the result of ADC_CountsTo_Volts().
The analog pin will not affect your voltage divider because as an input (as you use it) it is high-Z, but the input to the ADC is 180kOhms.
You might consider using a buffer amplifier which will provide an input resistance in the MOhm range.