ok took me a while to check them, but in hl4, intervening so karen lives switches on the switch 1278, finishing the quest in general sets the variable 590 to 12, thats what your stuff looks like right now since you did the quest after finishing paragon.
now, for karma files, the variable for the main story itself should be fine. the beasts variables (761, 762, 763) for karen alive route are set to 4 after finishing it, and the variable DOTW (769, no idea what it means) to 7
that might not be all but its what i got by checking with rmxp