I think my rep of Council of Exarchs is exalted long time ago, because I also have Council of Exarchs Tabard, which requires exalted rep to buy. However, when I log in TWW a few months ago, I see my rep of Council of Exarchs becomes friendly. I lost both exalted reputations for Council of Exarchs and Sha’tari Defense. I have the exalted achievements back to 2018 and 2019. They are still not fixed today (December 2024). Anyone else has the same issue?
I don’t recall seeing someone mention the Alliance reputation factions from the Warlords of Draenor expansion, but I have seen plenty of threads discussing how old reputations have been (apparently) randomly reset ever since Patch 11.0.0’s release in July.
You could try opening a ticket, but keep in mind that other players that complained about the rep reset bug have yet to see their problem fixed.