wow.... This is my 5th war, and I thought I saw everything.... apparently not.
Anyways, lemme give my 2 cents on this matter.
First thing first, if a desync happens, there is no clear resolution of the game, neither from the player's perspective, for from the WM's. From the point of the desynch, everything is murky. AI plays badly, players forget to take screenshots etc. I even heard that the AI draws completely different cards than the players, so even if both players play it out, they won't be seeing the same cards in the same order. So the correct thing would be to from the point of desynch, compare the two decks and decide who is te winner, but in that case, what is the point of playing the game through? Unless the desynch happens in the very las few turns, who is to say what could have happened?
The other thing is, and I really don't wanna talk about this, because I hate the thought, but if a series of desynchs happens for no apparent reason at all, one cannot help but have some nasty thoghts about the other player's intention, especially if the desynch always comes in a particular player's favour. I was in this situation this war with bogtro, where we had lots of desynchs and they mostly seemed to help me. I know that I did nothing intentional to cause or exploit those desynchs, but even so, if I won that duel, bogtro may have had some nasty thoguths, and with every right so. I would have certainly felt ashamed as well.
I think the keywords in a situation like this are honor and fair play. If a player starts his match with the best intentions, then I think he cannot do anything but to expect the same from the opponent. I think in a case of a desynch, the nice thing to do is to offer a rematch, regardless of the state of the game. After all, as the current situation indicates, there is no strict rulng regarding desynch. WMs are just as in the dark about the ordeal as the players involved.
To warp up, I think there is no correct WM ruling in a situation like this (it is no coincidence that the most debated WM rulings I saw were always involving desynch). I feel that it is the players who sholuld come to a honorable arrangement, and I think the honorable arrangement is these situations is a rematch.