Changed my shaman to an Earthen and I am missing Orgrimmar, Dark Spear, and Thunder Bluff reputations. The NPCs appear as neutral and I cannot benefit from rep discounts.
Bilgewater, Dark Talons, Huojin, Silvermoon City, and Undercity are working fine.
Same for me my friend, they’re just completely gone from my reputations tab. I’ve tried doing dailies, talking to npcs and doing tabard dungeons runs but none of these methods are giving me any rep for the missing three factions. Hopefully when they fix issue they don’t constantly reset like the Dark Talons did/do.
My Horde Earthen, made on the day Earthen were available to unlock, only has a few Horde reps listed on their rep pane. I have scrolled to the very bottom of the rep pane in this image:
Orgrimmar and a few other Horde reps are missing. Oddly, I talked to a guard in Orgrimmar and got the message of “You are now neutral with Orgrimmar,” but it still didn’t appear on my rep pane. That message has only appeared once.
I also did the Orgrimmar fishing and cooking dailies and got no Orgrimmar rep. Instead, both quests list rep gains in a few other reps, including a general Horde one:
For reference, this is my Earthen character if it helps with anything:
Also for the record, I have never used addons.
If there is any other information I can provide to help fix the bug, I will be happy to do so to the best of my ability if requested to.
Hopefully this will be fixed ASAP. Thank you! 
Same issue. Created Earthen, ran around got the “Neutral to Orcs and Tauren” messages, reps still don’t show up. Now, I haven’t tried using a rep tabard in a dungeon run yet.
This has happened to my Earthen as well, for Classic City reps I have Huojin, Undercity, Silvermoon, and Bilgewater; but no Thunder Bluff, Orgrimmar, Darkspear even after throwing on all ther rep tabards and going through Classic Dungeons.
I checked my Horde Earthen’s rep after maintenance today. Still the same problem as mentioned before.
Hoping this is being looked into, as I usually level alts in Cataclysm areas to get rep for the Horde/Alliance factions. Can’t really do that if I don’t have the reps in my rep pane, unfortunately. 
And if it is being looked into, thank you!
Rather than reposting my post from yesterday, a link to it: [BUG] reputations and Earthen
Logged in today, September 10th, 2024, after the long maintenance and checked my Horde Earthen’s reputations. Orgrimmar and a few other Horde reps still missing from the screenshot I linked a few posts above are still not listed.
I did check a few Horde Earthen profiles on the forums for those that created them and didn’t race change, and their rep section are all the same with Orgrimmar at Neutral (0 out of 3,000) while some other Horde reps they have are much higher than that. Thunder Bluff is another Horde rep that is not able to be raised like with Orgrimmar, with it being Neutral (0/3,000) if anything on Horde Earthen profiles. It seems like a thing that is affecting Horde Earthen as a whole is my best guess, though I don’t know how race changing into a Horde Earthen affects it.
I hope that this is something that has been noted and is being looked into, as I haven’t seen any official comments about this problem or any articles on it that I have noticed. As I said, I’m very frustrated that I can’t work on Orgrimmar rep for my Horde Earthen, among other Horde reps like Thunder Bluff.
Hoping this gets looked into and fixed ASAP. 
Wanted to make an update post because I took some screenshots of other bugs involving missing Horde reps for Horde Earthen.
This was all done September 13th, 2024.
I mentioned that I talked to an Orgrimmar guard and got the “You are now neutral with Orgrimmar” message, only to have Orgrimmar still not listed in my reputations window. I went ahead and talked to a Thunder Bluff and Darkspear Troll NPC and got similar messages, along with those reps still not appearing in my reputation window:
I also talked to a Dracthyr NPC in Orgrimmar, got the message that I was now neutral to Dark Talons, and that rep appeared in my reputation window:
However, after logging out and questing, Dark Talons was removed from my reputation list:
Oddly, I could talk to the Dracthyr again to have it be added again, but it is removed when I log out:
This does not happen with Orgrimmar, Thunder Bluff, or Darkspear reps. That message only appears once and does not appear again when I talk to a NPC of that rep. Those reps also never appeared in my reputation window at all.
You may notice that I had Neutral with the Frostwolf Clan rep, which I got from questing in Hillsbrad Foothills, and then it disappeared. It is no longer listed in my reputation window currently and I believe it disappeared when I logged off. I took the screenshots in a different order than I listed and only noticed it as I was taking them.
I’m guessing that rep is having the same problems with the Dark Talons rep. It’s possible other Horde specific reps do the same thing. I don’t know if getting any rep with them will keep the rep in the reputation window, but I’d be worried about it just disappearing and resetting even if I earn rep for those factions.
If I see anything else that I can report on this bug, I’ll be sure to do so to help out. I’m still hoping this will be fixed ASAP so I can work on my Horde reps for my Horde Earthen. Thank you!
Still missing.
As of 9/26/2024, Horde Earthen still are having a problem with Orgrimmar, Darkspear Trolls, and Thunder Bluff reps. Thought I would also do an update post.
So about a week roughly before the last maintenance, I talked to a Darkspear Troll and Thunder Bluff NPC to see the “you are now netural” message pop up again, though both of those reps aren’t listed in my rep pane:
The messages don’t appear again when I log off and talk to the NPC’s. It’s similar to how this happened before.
For Dark Talons rep, it did pop up a message of being neutral as before, with the rep getting added to my reputation pane again:
This time, however, the rep has stayed in my reputation pane when logging off instead of being removed from my reputations pane. I even checked today (9/26/2024), and it’s still there at 0/3,000. I have not tried to earn rep with them to see it that still stays or if it resets.
And because those three Horde reps aren’t listed in my reputation pane, there isn’t any way to earn rep with them. It doesn’t record any supposed rep gains in the background. Doing Orgrimmar cooking/fishing dailies, for example, just gives a generic Horde rep gain message that doesn’t affect Orgrimmar rep:
Interestingly, on my Horde Earthen’s reputation page on the armory website at the time this post was made, it has the missing reps listed there, but all at Neutral 0/3,000 despite not appearing in-game. You can see my Horde Earthen’s armory rep here:
I checked random Horde Earthen characters’ armory pages from the forums and none of them have any Orgrimmar rep that is above Neutral (0/3,000) with Darkspear Trolls and Thunder Bluff not listed on the pages I’ve seen.
I know there are plenty of bugs lately, given all the extended maintenance we have been having. I’m still hoping this bug is still known by Blizzard and is on the “to-fix” list somewhere. It’s just honestly frustrating to not be able to do things I like to do with alts like working on their faction’s main reps, and to see weeks go by without a word on whether this is a known issue or not is worrying.
If there is anything I can do to help out or test out, I will be happy to do so if requested. To those who are looking into and attempting to fix this problem, please know that it is very much appreciated.
Thank you!
I just got a “You now neutral with the trolls” and though cool they finally fixed this. Looked at my reps, nope, still not listed. Still busted.
As I recall, we were a year into Dragonflight before Dracthyr could gain Kirin Tor reputation and a few others, don’t remember which ones off the top of my head.
I’m having the same issue
I don’t think the missing rep is exclusive to Earthen or even Horde for that matter. A lot of people have been complaining about Bloodsail Buccaneers rep being completely missing and no one wants to eff up their Goblin reps to see if it will come back. I myself am missing it so unsure how that will impact getting Insane in the Membrane as I was just waiting for the anniversary rep to do Ravenholdt. I actually only noticed this after making the mistake of removing my Baradin’s Wardens Tabard whilst doing old content that required me to strip so as not to kill a boss too soon. When I tried to re-equip the tabard I was met with the red words of doom “You do not have the required rep for this item.” Funny how the tabard says SOULBOUND right on it and you can’t even purchase it without said rep.
Still missing the horde reps listed here as of 11.0.5 patch
Still missing and just found out this was an ongoing issue… having known earthen had this issue I would’ve chosen another race…
Wanted to provide a note that I recently race changed my earthen and the reputations came back as 0/3000 neutral so if you were non-earthen and paid to change to earthen, the rep you had is gone. Not a big deal to me for the classic races since you can put on a tabard and go at it but still a bit annoying.
My guess is that they made Earthen (alliance) first then copy/pasted them to Horde and forgot to change Stormwind, Ironforge, and Gnomeregan reps to their respective horde versions. I have no basis for this and I am not a coder but I did stay at a Holiday Inn last night.
I just noticed Orgrimmar, Thunder Bluff, and Darkspear are all missing from my rep tab, and I’m now neutral on all three after race-changing.
Just add this to the list of things deleted by the expansion. Assorted guild banks, warbank gold, warband currency transfers, honor levels, and random(ish) reputations. These things didn’t happen to everyone, but it’s happened to several thousand players, perhaps more and its just gone unnoticed. If this is anything like all the other data corruption/deletion issues, don’t get your hopes up that anything will be restored. It really sounds like they don’t do player data backups anymore sadly. At least they didn’t reset your reputations to absolute 0 (aka straight hated). Would make city visits very awkward.