So I'm in Act 1, playing on the side of the Watch, the quest to rescue and escord Fihelis, and there's just one little problem.

Fihelis is nowhere to be found.

All guides point to a particular room on the second floor, but he just isn't there. He's not in the house at all in fact. So, uh... what? Why? What triggers this bug? How can I avoid it?

Don't leave the estate once you enter because that's triggering this bug. Reload a previous save provided you got one and try again. Sadly I can't provide you with console commands to work around this issue because I wasn't able to find any online. Maybe you got more luck in case you really need them.

If only it was that simple. I never left the estate in the first place, not on that try, not on any of the following ones. I thought that maybe, maybe resting counts as leaving, got to him without resting once (which is not easy because that location is awfully balanced), but no dice, he still isn't there.

I would think that resting counts as leaving for whatever reason. Since you say you haven't physically left the location that's the only other possibility coming to mind triggering that bug. One of because there seems to be others in there as well which might cause him to disappear.