Do you lose your augs halfway through like in the Director's Cut?

Yes, you do get all your kit back at the end of the Missing Link.

Once you've finished the DLC, Quinn has left a box with all your gear in it, next to a cryotube you use to continue your journey (relax, there is a mission-marker on the hud on top of it.) (beware, I personally did not get back my old gear. but it might be because I already had an inventory full of stuff... so save before you open it. if you run into a similar problem, clear out your inventory. will edit this part when I find out what makes the box tick.)

It is interesting to note that the Missing Link mission now acts as a mid-game respec... for those who regret the choices in augments that they did early in the game.

Source: http://www.ps3trophies.org/forum/deus-ex-human-revolution/214740-directors-cut-answers.html