I'm pretty sure I caught this one, in both meanings. From what I can see, the bug goes like this:
1. Manually mark notification as "unread".
2. Get a second notification for the same thread.
3. Click on the bell. That automatically sets the new notification to "read" status (as it should be), but for some reason also sets the old one to "read" as well.
At no point do you have to open a thread for this to happen. (I sure know I didn't)
I haven't tested it fully, but my own notifications have been affected like that. Given that I started using them to bookmark the stories I am tired of, but was planning to come back to eventually, I am mildly annoyed.
The point I was trying to express with the previous paragraph (before it ran away from me in a different direction) is that I am not sure if only notifications past a certain age are affected like that or maybe there is yet another requirement for this bug to happen, as I had, in the past, threads I have notifications for update with new notifications without clearing old ones.
That said, in the past week or so this bugged behaviour became rather consistent, eating away notifications on 4 different threads. I would suspect a new forum patch to be at fault. And notification merging behaviour sounds like a good suspect, as it would explain why new notifications would affect the old ones from the same thread.
One more thing: I don't have like notifications enabled, so I am not sure how they would affect anything. I am talking only about "new chapter" notifications when OP of a particular thread posts a lot of words.