I disagree. If programs disagree on the status of groups, then
the only fair way to resolve this is to let them play it out.
You can't have either program saying
"well, those stones are dead but i can't be bothered to show it".
If the problem were genuine disagreement, I would agree with John. But
it isn't. Some bots have game-end-handling code which is much worse at
assessing status than their actual playing code. For instance, LeGoBot
plays at around 20k, but in its first-round game, it claimed at the
game-end that its one-liberty black group, entirely surrounded by
unkillable white groups, was alive. LeGoBot's playing engine knew it
was dead, the error was merely in its scoring engine.