The only thing that carries over from playthrough to playthrough is whatever weapon code you put in the locker after leaving the mines and the ability to unlock ending E, as far as I know. I'm pretty sure each playthrough is determined by what decisions you make in each. I've unlocked A-D so far with no problem.
Hahaha, I hear you! I was misinformed and told you couldn't get the achievements for doing all the side quests on your first play through because of Digging Up the Past, so I did all but two of them on my first run. :( I think you can clear your cache and memory to re-input the code, but you lose your replay counts.