I lost reputation with The Unshackled after the expansion came in. I was already Exalted, farming the paragon chest and noticed that the reputation went back to neutral.
Same here.
I made a post a while ago linking to lots of other similar reports: Reputations Reset From Exalted to Neutral - #17 by Cixel-illidan
I think the resetting may have stopped, but missing reputation has not been restored, as far as I know. Hoping something is done about it soon.