How to switch between two DC power sources powering a motor on an electric vehicle?
I suggest that you talk to another professor.

I'm assuming you use an H-bridge motor controller to actually drive the motor. Without actually trying to implement it (that is, it may not work), I'd suggest that the controller has an enable input which will disable its internal drive. If you disable the controller just before you make the switchover, then reenable it just afterwards, the controller ought to handle the job.

Alternatively, if you provide a decent-sized capacitor at the controller input, it will provide current during the switchover. And while this is obviously impractical for prolonged outages, using MOSFET switches the switchover period should be measured in microseconds, and it's not hard to get a capacitor do that, even for fairly high currents.

Yet another possibility you might consider is to provide the two batteries at different voltages, with the high-demand battery (oddly enough) providing a slightly lower voltage than the cruise battery. Then you provide a switching circuit which looks like







simulate this circuit &ndash; Schematic created using CircuitLab

In cruise, the switch is closed, and since the cruise battery has a higher voltage than the acceleration battery, D1 is reverse-biased, and no current is drawn from the accel battery. If the switch is opened, the accel battery provides all the power.

The switch is used only to maximize efficiency. Some power is wasted during acceleration due to the drop across the diode (which is why a Schottky is specified), but this is only true during the relatively brief periods when high acceleration is called for. It also has the virtue of allowing the accel battery to act as reserve battery, just in case the cruise battery is exhausted during use. 

It's perfectly possible to replace the switch with another diode. In this case, high current draw will hog down the cruise battery until the accel battery takes up the slack. This has a couple of drawbacks. The first, and most obvious, is that there is a continuous power loss due to diode heating. If you use a high voltage (and therefor lower current) battery, this will minimize the problem, but it may still be objectionable. A second, and less obvious difficulty is that as the cruise battery is discharged its voltage will lower, and the accel battery will be accessed more and more, until both batteries run out.