This article however is about stories that disappear without receiving either.

Here's an example of a submission that does not include the [flagged] label, but which has a moderator saying it got flagged, and that the flags are the reason it's not on the front page. https://news.ycombinator.com/item?id=13741276

Many months ago, I had several submissions that were visible when I was logged in, and yet when I accessed HN as a guest, they were not in the submission ranking.

From what I've seen mods are happy to fix any problems.

The moderators bury things on the front page pretty routinely.

That's a pretty big (and vague!) accusation to just throw out there, especially in light of this comment elsewhere: https://news.ycombinator.com/item?id=13858327

dang 6 minutes ago

As others have pointed out, the [flagged] annotation means heavily flagged. A story can be downweighted off the front page by user flags long before [flagged] shows up. Indeed that's what happened to the submission the OP is complaining about. Moderators never saw it.