Rodgers admitted that if they went over (and he did say he was fine if they went just over the 13.5 line, to the next hash) they ran the risk of the Refs intervening and undoing their "hard" work.

The ball boys are always rearranging the balls, into and out of the case they are in. They have towels and are always rubbing them down. It could be done on sidelines. Riskier, however, because you could get caught on camera with this method.

Bathroom break makes sense, but after NFL and Wells investigated for 4 months, they came up with not another instance where the balls went missing before the game. And you KNOW they asked the Head Ref for each Patriot game that year. That is why the bathroom break seems like such an outlier. So rare it has to be unrelated.