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I'm trying not to read the spoilers/walk-throughs etc. I'm at the point where I can go sail a ship and start chapter 4. If I haven't completed all the quests for my class, will I lose my keep if I sail away ? (or, eg, as a thief, sail away and can't make my dues to the guild)
I would finish all the quests for your keep because they are interesting and sometimes there is a reward at the end. I hope that isn't too much of a spoiler for you.

Don't worry about your stronghold when you leave, it will be taken care of for you.

Hope this helps
The only one that you can actually lose during the boat trip is the Thief stronghold. Your dues to Renal are suspended during chapters 4 & 5, but it's still possible to lose it due to how the timers work, and the fact that the boat trip takes several days. It's best to leave on the boat immediately after paying off your guild contact. Also, as soon as chapter 6 starts, the timer for the dues starts back up, so you should head for the guildhall immediately or you might lose it then.

All of the other strongholds are worry-free. If there are more stronghold quests when you leave, you can do them when you get back in chapter 6. But don't leave any messengers hanging. If somebody tells you something about your stronghold requires urgent attention, do that before you leave.
Roughly speaking, from chapter 4 on, the main quest takes precedence over the side quests. I usually have all available side quests finished in chapter 3, because then you don't have access to Athkatla and the Amn locations for a long time (and when you come back, there will be a couple of new stuff to take care of...).
Hope this helps!