Don't bloody fix them. This is probably the less popular opinion, but unless you're willing to write an algorithm that will adjust every prior score to account for the bonuses at that time, you are throwing a wrench into the war and changing the parameters mid-war. Which is definitely not cool at all.
Now, that million point lead on the leaderboard? Nowhere near as big as it was before. Some folks have gemmed their hearts out in some fights all across the board, and now the points gained per refill has skyrocketed.
Seriously, if you're going to not QA crap to make sure it works out the gate, keep it in your pants. There's always a next war. I mean, it is blatantly obvious that the entire playerbase is your QA, but quit treating us like beta players for your game. We're not.