When Imoen was stolen from me in BGII I was stunned. Therefore my main goal was to get her back. By doing this I ignore the all the quests outside the cyty of Athkatla. Now I'm in the underdark and Irenicos has alredy stolen my imortal heritage, and this seems to make me ill. Is there time to complete the quests like De'Arnise hold before I recover my heritage?

Yes, you can continue with your side quests in Chapter 6.

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I also ignored most of the quests first run, but the game timeline only "moves along" at chapter changes, so you can spend a year doing subquests in chpt 2 without having Irenicus "experimenting" further on Imoen. Not like she cares with the AI(don't i sound cruel!?), so take your sweet time going to chpt 4 if you want.

yeah the first time i played i was worried about the time limits and i only did enough side quests to get my 20,000 and get after iomen. then i played again and realized that there are no time limits. so i just kind of deleted that game and started over. it was a bummer but worst things have happened