Yep, the search rebuild is not something to write home about. Beta3 should have some improvements on this.
It doesn't remember where it was, so it will have to be done all over again. If you can stay logged in.
I still haven't completed my 750k forum, or ANY of the ones with millions of posts.
I have made some changes so that if you're logged off, when you login everything will pick up from where its left off. However, I'm trying to figure out why you'd be logged off in the first place. Each page view should extend the amount of time your session is valid for (and it's currently valid for an hour, I think).
(Leaving this bug here, as hopefully I can figure out why that's happening...)