Note, there's some spoilers ahead, so if you haven't finished the Clan Karga/House Skeldon quest lines, you might want to stop reading here.
I decided to side with Karga Clan in the missions, but I didn't get around to rescuing the girl that Ebrat Skeldon has locked up. I snuck into one of the guy's house and took the counterfeiting plates as evidence, then went back to Ultar with them. He thanked me, and I got the relic I wanted. I went back to the Excavations area to find it completely devoid of any NPCs, including the girl. The quest lines for her didn't disappear though, I can go back to her husband and threaten him into stopping the flow of information to Clan Karga, but this quest line seems to be left dangling.
Is this a bug, or have they just moved the girl somewhere else and I can actually complete this?

I think that by giving the evidence to Ultar you effectively ended Skelden House presence in Thalmont, so they (Skelden House) are gone and any unfinished quests involving them will remain unfinished.