I had a look at my reps today and found a lot of them missing, but after Googling found that by talking to the NPCs of those factions I could get them back in the list.
This hasn’t worked for Artisan’s Consortium, but I figured I’d try some different NPCs later.
One I particularly cared about though was the Obsidian Warders, with which I was halfway to exalted. No amount of talking to NPCs belonging to that faction brought it back, and I had the same issue with the Maruuk Centaur, which did return when I got some rep with them.
So I did some dailies for the Obsidian Warders, and have now lost all my progress. Great patch.