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Seems to be a regression, not sure if devs are aware. Notifications seem to come back randomly, or sometimes don't disappear at all when you view the topic. Marking all as read usually fixes it. Seems to be an issue with actually reading the topic.
There was a bit of a refactor of how the unread system works (previous system took too much of a toll on the DB)
Side effect is that for a few days after you upgrade, you might have some anomalies with unread posts (we didn't bother with an upgrade, because it really wasn't worth it)
It should settle down in a day or so, if it's still going wonky for you then let us know please
@psychobunny okily dokily, thankily dankily.
Actually I found a bug just now and fixed it, https://github.com/NodeBB/NodeBB/commit/5ff293109d90dae5345b3afa7fbe8679550485d3 it should be good from now on.