I would be inclined to remove the battery leads on a vehicle that is fitted with sensitive electronics, but I don't think that the Bongo is, or at least the early diesel versions anyway. Not sure about the petrol versions.
I once had a Smart Car, and when the battery went flat I connected a 12 volt power pack to the battery to start it. For some strange reason it blew all the dashboard electronics and I had to have a new speedo cluster fitted. Cost me a fortune. I deliberately only used a power pack, and not a boost charger as I was concerned about the electronics, but it still didn't make a difference. With hindsight I should have called out a breakdown organisation to get me started, then I would have had someone else to blame.
