When you reach the point in the Thieves Guild that Tonilia will upgrade a piece of your Thieves Guild gear, after you select one, it gives you the option to finalise it, or the option to go back. The message reads “Actually, let me chose something else,” even though it should read “choose.”
Also, I’ve completed the main quest including Season Unending, progressed most of the way into the Civil War (actually, having to postpone the civil war that I had already been doing) and the Jarl + Steward that the Stormcloaks installed for the brief moment that they had control of Markarth and the Reach went to the Palace of the Kings in Windhelm as the others do (as I see your mod has done with others). Bothela from the Hag’s Cure, rather than send me to the actual Steward, sent me to the Stormcloak Steward Reburrus, who doesn’t even have a voice line for the quest. Also, Thongvor Silver-Blood is still reading as Jarl, even though he obviously is not. Their dialogue, since I haven’t talked to them before, are indicating that they are still in Markarth. I only have a handful of mods and I don’t think any of them have caused this. Assuming this is the case, and that none of my mods are simply preventing things from loading, I think your patch should prevent Bothela’s quest from starting if the Stormcloaks are in power, and should only ever point to the Imperial Steward, and obviously that they should go back to their houses and Thongvor’s title should revert when dethroned.