You might not have "show dead" enabled in your settings. There is an antisemitic comment that was flagged and is now "dead" with a bunch of replies - so you would have seen those, and then now not see them if you don't have "show dead" enabled.

I think that with showdead off, if a flagged comment has non-flagged replies, the toplevel comment will still show up as [flagged] and the replies will be visible. Flagged comments are usually collapsed, though, which might be why it seemed like the discussion tree disappeared.