While looking into this issue, I saw earlier mentions of the same problem affecting Dark Talons and Obsidian Warders. The post below is from December 2023, and from the looks of it, I can’t imagine this being anything other than the same issue we are currently experiencing.
This post even mentions instances from 6 months prior.
Some people also mentioned losing Voldunai reputation. Comments relating to this issue can also be found on the Wowhead Voldunai faction page from patch 10.0.2, dating back to December 2022.
Since this problem bothers me deeply, as it does you, I feel uncomfortable not knowing whether it will happen again, and it makes me uneasy to play the game and invest my time into it. I logged into the beta today to see if I could replicate the problem there. I went into Hellfire Ramparts with my Blood Elf Rogue to gain some rep with Thrallmar and test the issue, and I managed to replicate the same problem. This means the issue is present in the beta build as well. I wasn’t sure if it was normal for reputations to reset in beta, so I gained some reputation with Lower City, relogged, and can say with confidence that Lower City wasn’t affected, but Thrallmar was.