I have exactly the same problem. I hope this get solved soon in a update.
If no update is coming then our only change is:
Hoping for a prestige kind of thing (reboot the nanosuit) and hoping all challenges, weapons en perks get reset so you can unlock them again. If not then i think i can never unlock it because a kind of the same happened with Battlefield Bad Company 1 and 2, also never solved!
Limited Edition keeps the Hologram Skill Assessment challenge locked! A bit of a problem if you like to play games only on 100% completed! The same happened with some Battlefield Games.
First time i pre order a limited edition game in my game carrier for the extra's. But there are no extra's only a unique dogtag but this cost you the hologram challange! And i payed extra for this limited edtion 10 Euro. I can say i have lurnt my lesson, Never buy a limited editions because the only thing you get i some few extra problems all for just 10 Euro!.......... But after all Crysis 2 is still amazing game.....