Use a Dremel Moto-Tool fitted with one of the thin brown cut-off wheels. Heat sink the shaft between the place that is to be cut and the stepper motor end plate with a small vise grip plier clamped lightly on the shaft. Use high RPM and cut slowly so as to not overheat the shaft excessively. I have cut off the hardened stainless jaws of a digital caliper with relative ease, so the stepper motor shaft should not pose any problem for the cut-off wheel. Just try not to bind the wheel and break it, and use eye protection in case it happens.
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