In theory, all "stronghold" quests are suspended in chapter 3 and get picked up after you get back. I say in theory, because while it usually worked well, I had at least one instance where I came back only to find the people affronted and telling me to leave. It was really annoying, too, because it was my favourite - the Ranger's Cabin.
But all in all, you should be fine. Thieve's Guild is the most disappointing of them anyway.
: Of Magic and Macaroni - a blog about, well, a witch in the kitchen.
The Pale Mansion
: My e-published lovecraftian novella! You should totally check it out!