I see new topics flagged to the moderators by Akismet after people have replied to them, I also see them flagged when they are up to a day or so old, with or without replies. It is clear that Akismet takes up to (at least)* a day to flag a topic, so in that time users can see it, reply to it, move it, whatever, then it disappears, either temporarily if a mod says it's OK, or permanently if it is ruled to be spam.
When @sterretje first asked this question I thought it very strange as I had not noticed the problem. Alert to the problem I paid more attention but it never happened to me. Now I know why, as I am a moderator a topic does not disappear for me, it just gets flagged and I see the flag, I can still see the topic. You and @sterretje , not being moderators but having the ability to move topics, only see part of what is happening. I suspect that you might also notice that you might reply to a topic offering help then it disappears for a while only to return later. If you see this then I guess it's the same underlying cause.
* I know! That's like the idiotic marketing claims: 'Up to at least 50% off'!