User blog comment:Itachou/The Missing Link overview/@comment-83.84.227.208-20110918125128/@comment-3518353-20110920003310

If you read the thing over again, it says that you get to essentially create a whole new character or just redo the one in the main game if thats what you want to do. I'm assuming that Belltower takes some kind of power source or code from Jensen that deactivates his augs so sometime int he first third of the DLC they have you go get it back. You don't lose augments for the whole game, just part of it. To do otherwise would be a big gamble for a game that already has some really bad boss fights.