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Have encountered this a few times in this game now.
Have triggered Daenerys return and am vassal to her.
after much play, have taken Weeping Town from Dorne.
Placed a garrison of about 100 troops.
Character was in the town helping with defense with about 290 troops.
Fought the siege. My character was taken out, but defenders were victorious.
Get message that battle is won but siege is not over.
Enemy armies depart in shame.
In town menu, select Wait here a while.
A few moments later, town flips from Targaryen to Dorne.
Sometimes there is an enemy noble occupying the town, sometimes not.

I am unable to hold Weeping Town against siege due to this. every time I successfully defend against siege, it switches to enemy faction owned a few minutes afterwards.

Some more info and a correction.
Correction: my lands recruit Northmen (birth culture) not Vale (first ennoblement culture)

Converted my character to the Seven and can now recruit in some of the Reach, Westerlands, and Vale. My first Vale fief of Crab Bay is an exception, forceful recruitment only even though relation is 63.
I can recruit from some villages of my own villages which seems strange given that character now worships the Seven and troops are Northmen.
I am now blocked from recruiting in some of the North and the Freefolk lands. Interestingly, Nightswatch villages changed from "Recruit Villagers" to "Forceful recruit"
I am still welcome to shop in the faction armor for the North and the Nights Watch. Also, my wolf still likes me well enough.
so...it does seem to be tied to the religion code somehow. again I hope this helps and good luck in the fix

I am also running to recruitment issues. I have a character who was from the North, joined the Vale then recanted and set up shop in his own kingdom.
I can recruit from the North and from the Freefolk. I cannot recruit from the Vale, Westerlands, or the Reach. I have not tried changing religions yet.
I can also not recruit from my own villages, I assume because they are Vale at this point (I believe recruitment troop type follows your first ennoblement, not your land of birth. I learned this in a previous game after starting a kingdom in the Icy north and found that I could only recruit Freefolk in any territory I conquered)
Hope this helps. Produno, this mod is awesome and really has great immersion and play. The skins are fantastic, the cities remarkable, and troop balancing impressive.