Submitted bug report multiple times and nothing has been noted about it, have also seen it on the forums in other spots, but reputations are missing or reset to neutral. I have all the Dragonflight & The War Within reputations at max renown, and on login I have to go to either an NPC for that reputation to have it show up on my characters reputation pane or get rep gain (only for it to remove on logout a short time later). However, I noticed one day that I did a world quest for Order of Embers and it said 75/3000 neutral. I thought for a second that I had completed it to exalted and sure enough I have the exalted achievement. I also checked on a copied character that I had on PTR for initial 11.0 patch testing and that character has 4720 rep into Paragaon. I completed every quest on this toon, I have the tabard collected and can not get the rep without grinding thousands of world quests.
I know it’s probably not possible to get the reputation added, but at least some kind of acknowledgement that it’s being worked on.