I believe you are asking how you can make sure the absolute encoder reading will be the same after you reassemble the motor and encoder as it was before.
If you have the capability to apply a voltage across any two phases now, this will force the motor to a known shaft angle (like a stepper motor). Read the absolute encoder position. When you re-assemble the motor/encoder system after repair, turn the encoder so it reads this same position. Apply voltage across these same two phases when you re-attach the encoder.
Curt Wilson
Delta Tau Data Systems