Is there a workaround for a Hall effect encoder out of alignment with its sensors on a small motor?
Source

Once the board is soldered to the motor, the magnetic encoder disc can
be pushed onto the motor shaft. One easy way to accomplish this is to
press the motor onto the disc while it is sitting on a flat surface,
pushing until the shaft makes contact with that surface.Pushing the
disc a little closer to the PCB can ensure strong signal and good
performance.

You could use a flat surface with a hole to push further or to put it on bench vise.