Supercapacitor bank charging process breaks down dc/dc converter
The problem is the fixed 15v output voltage of your DC-DC converter. Capacitors should be charged with a current output, not a voltage output.
If the voltage on a capacitor is less than the output voltage of a power supply feeding it, it will take as much current as the supply cares to supply, in other words it behaves like a dead short.
The DC-DC converter can still be buck, can still use the same power stage, but the controller should be changed to control the maximum current output to safe levels, as well as the maximum voltage to be safe for the supercaps.
With regenerative braking, ideally you would program the converter to put a braking torque on the wheels proportional to the position of the brake lever/pedal. This is naturally what you would get if you try to mimic the response of how mechanical brakes would behave, I presume you want the electric system to behave as a driver would expect it to behave.
I blew a buck converter up (42 volt rated) when I had an input supply inductor that was intended to smooth out voltage pertubations. Ironically it worked just the opposite; an output short circuit (intentionally applied during a test) when removed caused such a sudden change in the input current that the input inductor produced a voltage in excess of 42 volts and bingo, the Linear Tech device failed and went short circuit from the input to the output i.e. the MOSFET that did the switching broke down!
So, what might be happening here is that when your switch kicks in, you rapidly charge the chip's input supply decoupler cap and a high current pulse exists as this cap charges up - if there is any appreciable inductance in the line feeding the switch from the AC/DC converter, as the cap input current starts to fall off (because full charge is approaching), the inductor will attempt to keep this current flowing by raising the potential on the buck-converter side. I can envisage that same scenario happening with my old design but, I got rid of the inductor and never tested that scenario specifically.
Most decent buck regulators have got short-circuit protection built in so, if you don't think the problem lies in the output try and think about the line inductance from the AC/DC converter, thru the switch to the buck regulator.