Right off the top of my head, you'd have to use two separate controllers to switch between 48V / 96V. There are other land mines you might step on in that particular field, but I don't have any experience with that.
A long time ago, when all that was readily available was low-current batteries, there was a lot of discussion about delta/wye switching. Normally the six wires coming from the three groups of motor-phases are configured inside the motor housing, and then only three wires are run out the small ID of the hollow axle (either delta or wye, never both). If you are using a non-hub, it would be easy to experiment with separating the internal terminations (time-consuming, but not difficult). Then, you could solder thick wires onto the phase-group terminations, and run all six wires to the outside of the motor.
Delta-terminated phases will run faster for a given voltage, and wye is slower, but...it draws fewer amps at lower RPMs, so it would be easier on controllers, plus easier on a low-amp battery pack. I seem to remember that wye also has less inductance (?), so its easier on RC controllers, also small E-bike controllers. The Delta/wye speed-per-volt ratio was somewhere around 1.7:1, which would be a much more useful ratio (compared to 2:1 between 96V / 48V), and easier to achieve than voltage doubling (one controller, one system voltage).
Just a theory at this point, never had any need to try it out. I'm sure there would be unexpected problems arising...
Increasing the amps to the motor will make the motor and controller briefly hotter, but if the motor is big enough to accelerate up near its top-speed, it will have time to cool off at low amps...in this scenario, more amps will improve how hard the motor accelerates (fast acceleration as opposed to slow acceleration)
