I would imagine that would work, but I think you'd want to make sure that the steps were in phase/sync with each other before you inserted the longer shaft. That or either you may end up with some odd jumpy sketchy rotation, or potentially motors that actually fight each other. I don't know how many steps per revolution a hard drive motor has or if they vary from model to model and that could be a point of concern as well.
If the specs lined up you might actually tap out the shaft and then just connect both motors up to a battery to hold them in place while you tapped the new shaft in. Use the same stepper controller for both sets of leads and all should work.
Disclaimer: I have never actually done this. I have only taken the time to look into it because I was going to do the same thing myself with larger stepper motors. My steppers just didn't have the same number of steps/resolution so I figured I was out of luck.