It seems you went through quite a learning curve in only just a few hours.
Big capacitors directly on the USB bus are bad because of very high surge currents through the connector at the moment they are not properly mated yet.
Just take a regular power supply with banana cables and put it's output voltage directly to a big cap. Currents can be so high that a (very small part) of the metal melts and the banana plug welds to the capaitor wire.
On the other hand. Big buffer caps are good for motor drivers.
A simple option is to add a small P-channel MOSfet in the 5V USB line and switch it very slowly with an RC on the gate. Just extending the charge time of the bulk Elco to 10ms or so makes a significant difference, but ideally you should keep the charge current within the USB spec. If this MOSfet switch is under uC controll you can also turn it on only after the connectors are properly mated. With these precautions you can easily put extremely big capactiors on an USB bus.
Or you put a resistor between the Raw USB input and your buffer elco's (Few 100 Ohm) and turn the MOSfet on to short that resistor once your Bus voltage has risen far enough. (See ADC below).
A big bulk capacitor also flattens the voltage peaks when the motor is braked.
Your motor has an encoder, and apparently you are already monitoring it's speed. With a properly implemented PID control there will be no more high current spikes or abrupt braking, and no need to add more hardware to mitigate this.
But during testing, or when the PID controller fails and the brake energy is so high that it can be problematic a very common way is to add a brake resistor with a (MOSfet) switch over the Bulk capacitor.
These brake resistors are very common with high power 3-phase inverters of multiple kW.
Just typing "brake resistor" into Ali gives a whole lot of hits:
https://www.aliexpress.com/wholesale?SearchText=brake+resistorWith a small motor a beefy Zener is good enough.
Other options can be based on a TL431, a power transistor and a resistor, or you can measure the bus voltage with the ADC of your uC and turn on the brake resistor if needed in software.