I don't think this will help, but a couple of observations that I recently had that might have some bearing when you are testing:
1: I noticed that here must be a large capacitor in the controller or motor that retains a good charge when the battery is disconnected, so you may have to remember to discharge it before doing anything.
2: On the four interface battery connections, you have '+ A B -'. The '+' and 'A' are the same circuit, as are 'B and -'. I think the charger port that is on your frame is connected to A and B. If there was a short on your charger circuit, I wonder if that could have caused the arc that you saw.
3: If it were me, I might think about taking the battery connection board (I think you called this the 'discharge mount') out of the bottom of the battery compartment and disconnecting everything except the + and - and see if you continue to get the same problem, or perhaps not connecting it, making up some jumpers from 12 guage wire, and feeding 48V directly to the controller from a battery pack, thus bypassing everything that has the potential to short up to that point.
I have only been able to ride mine using an external battery as I am still trying to work out an efficient 52V build for 21700 cells in the Frey battery pack. That is why I am familiar with the circuit that those connection points are using. I was surprised to discover however, that on the very first time I powered my new bike up last Friday, the trip meter immediately reported it had 462km on it! Frey is looking into it, as they were also shocked that it happened, and have gone to Bafang to see if they have an explanation.