Okay so, I've been attempting to beat the game without killing anyone or being seen (ghost) in order to get both achievements. I just beat the flooded district and for some reason I was spotted little to my knowledge (usually I would just re load the game to my last save). As frustrating as this, I'm dedicated to beating it but my question was, if I "technically" beat the level and hit X to replay the mission again, will it mess up my achievement or will all be fine when I beat the level again without being seen? I hope this doesn't sound confusing..

You will be all fine.