ÃŽ agree with Luke: do not worry about the ball's value - once you punch it up, it's a dead investment. If you are familiar with an older piece of yours, a re-drill is IMHO a good opportunity to learn more about the ball, and how the layout changes its reaction.
The MB position should IMHO not be a problem - after all, it's just a marking for the core's primary rotational axis, not a vital element of the ball itself. A good ball driller will, after plugging weigh and measure the ball anew before a new layout is applied. If there's an MB shift, this should be taken into account.
Personally, I never had problems with plugged and re-drilled balls - cracking occured, yes, but mostly on thin-shelled, new equipment, and so far never on plugged ones.
I'd go for the experiment, when you already have an idea about the reaction you want from the ball in the future.