Those issues were hyped way up by the gaming media, I'm pretty sure rope kid's on record a couple years back saying that there's no bad blood between Obsidian and Bethesda/Zenimax and though they might want to negotiate new terms, they'd be perfectly open to working together again.
Plus, Pillars of Eternity was a pretty big success and they're already working on Tyranny for Paradox. They're in an inherently stronger position and can negotiate from that position.