jurek: Will he do this to all of the other hundreds of games that were improperly scored, too?
If I were him, I'd say no :)
I think that unless he's asked to change a specific game result all the results will be kept as they are now. It's very tough for a computer to determine the correct score in many games; that's why the players need to mark dead stones and let the computer determine the score from there. If the stones are incorrectly marked dead, the score is incorrectly calculated.

Binabik: it shouldn't be possible for this to happen, am I right?
Well ... you accepted the score.
If you had declined the dead stones the game would go on ... your opponent could mark the stones differently on the next move ... or maybe she'd mark them the same and you decline again ... and again ... and again ... and again :)
The end of game needs to be reviewed by Fencer. There have been quite a few threads about that already.