Quoted from Xerico:

It really depends on the machine. Some machines do not lose playfield power when the coin door is open. Some do.
Each machine and situation would have to be resolved in a manner that was fair to everyone. Even if that means that the loss of a beneficial situation means the loss of the entire multiball. If the player's ball drains and they lose the ball, PAPA rules would end that player's game on that ball and record the score. Then that player would get X balls on a new game where X would be the ball lost plus any balls remaining on the game.
So if this happened on ball 1, the game would end and the score would be recorded. Then on a new game, the player would get 3 balls.
On Ball 2, the player would get 2 balls on a new game. On Ball 3, the player would get 1 ball on a new game.
This second game score will be added to the first game score to come up with the official tournament score for the game.
At least, that is how I would rule on the situation.
Marcus