Robin2:
How does the hall effect encoder detect the motor position?...R
I don't wanna speak for the OP, but I use hall encoders in my job and they usually have two signals (sin/cos) with a 90 degree offset providing you exact position in an analog fashion. Once the sensor has been calibrated at a reference point to be 0 degrees you will always know absolute position. And the nice thing is that as long as you don't move the sensor mounting you never have to calibrate again and your reference position never changes even after restarts or new software.
Back to the original question, can you give a little more info on the motors in your project? If you're doing a differential drive then I am assuming you're using some kind of brushless synchronous motors? How are you controlling them?
Also when you say the sensors are "Calibrated on a given surface", what does that mean exactly? Does that mean the axial offset between the magnet and the sensor? Or does that mean the rotational offset being aligned to a 0 degree reference?