I do not think it is the least bit mysterious. Photographer sees a scene and makes a photo. A few hours later he sees an even more compelling version of the same scene after more cannon are fired. I do it all the time (well, not with cannon balls but you know what I mean). So does every photographer. I do not understand why they concluded though that the one with cannon balls on the middle of the road was the second exposure, but then concluded that those cannon balls were moved not additional cannon balls. A more logical explanation seems to me to be that more cannon balls were fired in the intervening period. This could easily also account for some rocks also changing position.
And even if they were moved by the hand of man there seems to me to be a pretty obvious explanation - someone said to the photographer something like, " boy you should have seen this yesterday! Those cannon balls on the side of the road were all over the road but they were moved so as not to impede traffic". If someone said that to me I might have been inclined to say, "well lets put them back, make another photo then move them back again to the side of the road...................................... " Maybe it is not kosher to do this to a hard core documentarian but many war photographers do this kind of thing even now. Frank Hurley a famous Australian WW1 photographer was notorious for posing shots to better convey the feeling of being there to a home audience. He got into trouble many times over it with the iconoclasts.