[Please note that I will yield to about anyone on proper interpretations of the rules.]
I wasn't really focusing on a particular ruleset. I tend to agree (as I indicated above) that the ko state should also be preserved if the scoring is rejected. This would also agree with the section of the rules you referenced. This game was under Japanese rules. Under AGA with the passing stone, there is no advantage to passing if there is any question of the status of any stones, like a ko. Same would also apply for Chinese, but here you would have to resolve to ko before you filled any dame.
The status of the white stones has no impact on the outcome of the game, I would have left them dead and accepted the score (and the win). That was already White by more than 90.
That being said. It IS proper to resolve all kos before ending the game. Fill, or kill, would have worked here.
Notes for future play:
- If you know you have lost and there is nothing you feel you can learn from continuing, you should resign.
- If you know you have lost and want to play to gain experience, ask your opponent if they mind continuing.
- If you don't know that you have lost, keep making the best moves you can.
It rarely matters what the score was. Usually, only the outcome - win, lose, or jigo (tie) - matters.