so how do they exactly work? in mission 2 I couldn't be ghost so have to replay that for it, so by completing that will I get the ghost achievement?

I just checked in it and saw we have the stats exactly how we had the first time around (would have been more fun to have the "overpowered" Corvo in the end game) so if I just play that mission and finish it then in my missions list the new ones will appear right? will that be counted towards my end or the save before the end game opening the door for emily?