I decided on war sides and joined up Robert's Rebellion against the Targaryans. This however made me, of course, temporarily "independent" - but also automatically turning me into a traitor of the Starks. My (former) liege, Ned Stark, now has a -100 negative modifier; he literally despises me (aside from treason, he also "desires my duchy").
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Is this supposed to go away after some time or through a save-load (it didn't)?
Do you have a save from just before you chose sides in that war you could upload please?