Umm... QRH to rule out or to confirm fuel leak, select totalizer or calculated based on your findings. As far as what to do after you land after your flight, consult your trusty MEL and you will be sure to find all the good stuff that needs to be done. ie: manual fuel drip check. I do believe that would involve an AME. Doing a drip check is one of the most fool proof ways of determining whether or not we used more fuel than planned and that was recorded by the FMS.
Short_Circuit: I think I agree with you, but to clarify bout not being concerned with being 'tight' on fuel, I know where I come from that we are not in the habit of carrying around loads of extra fuel for no apparent reason. Take what is required (due consideration to weather, anticipated traffic and contingencies); tankering only if fuel is at a premium at our planned destination. Drips are deemed to be accurate, that is where we would be making our fuel decisions from. Yeah? Yeah sure!!
Engine running while boarding and loading baggage? which one would you shut down? assuming there are no ground services I would also expect to be using stairs as apposed to an air bridge. Which one would you be shutting down? Suck the men and luggage into the engine or perhaps the little old lady with the poodle trying to make it to the stairs. I can see the headlines now... Poodle gets sucked into jet engine after chasing after owners wig! I'm sure this does happen in some parts of the world, but nowhere i have seen, and I've been to some rough places. That being said, I'm sure it does happen.
Solution... shut right down, deal with freight, start it back up, shut left down, deal with pax. Do-able, but come one... not the a/c designed for the bush now is it. Fuel... as far as I can tell, you might be able to reset the FMS by flipping the dates, or a couple breakers. Not sure.