According to the data sheet, the single-turn encoder also has a REF+ & REF- output.
Those should be the zero reference.
You can think of the motor as a bit like a single position stepper motor; apply power to the appropriate combination of windings and it will be pulled to a fixed orientation.
Gradually change the relative winding currents - like "microstepping" a stepper - and you can pull it through a fixed movement.
That should allow you to find the zero ref marker after powering up?
Some machine tool servos use encoders that only retain position with power applied and have rechargeable batteries in the drives to run just the encoder while power is off, so they retain the last position.