At some point either with the War Within pre-patch my reputations reset randomly for specific factions on my priest. This seemed to be targeted at faction-specific reputation.
In my case the 7th Legion reputation was reset to exalted and my Obsidian Warders reputation was reset to neutral. The latter of which is a pain to grind since it takes a time-gated dailies to get to exalted.
I was hoping the issue would be resolved by now but it still seems persistent. I have submitted several GM tickets regarding the problem but the answers given have been to simply submit a bug report when this has been an ongoing issue with players since last year.
I’m sure some players are not even aware they lost reputation from the pre-patch. I think its important for this kind of issue to be resolved, it is along the same lines of having a mount or pet randomly removed from your account.