After this point, I'm making educated assumptions based on possibly inaccurate recollections and probably faulty reasoning.
I say you to both yes and no. I don't believe that threads will start disappearing, no, but I do believe their order in the listing can get messed up. I don't think it's a matter of the "system" losing the posts/threads entirely, simply changing the order. That last bit I'm sure of. Story time:
The Greasemonkey Script thread was almost entirely busted a few months ago. All of the hyperlinks were broken because Duardo was a n00b and used the hyperlinks in the format of &postID=#, which redirects to the format of &prepeater=x#postID (IIRC, mobile right now, bear with me). This was bad because, as Achronos pointed out, -blam!- gets messed up in big threads, so the &postID links wound up giving the wrong page number, about 18 less than it should be, if my memory serves correct. For instance, say postID 5 took you to prepeater=20#5, in Duardo's thread, it would have redirected you to prepeater=2#5, but post #5 isn't on page 2, so there's nothing to go to, so the link would be borked. I fixed all of those, anyway, and concluded that something happened to lose ~18 pages of posts (or just put them somewhere else).
Actually, reflecting on what I just said, I don't know whether to look at that as "everything fast-forwarded 18 pages" or "what the hell happened to the missing 18 pages". I suppose I just provided some hands-on experience with this issue that you can all recount and do with what you will, because I'm tired and don't feel like thinking on this. I'll come back tomorrow.