Replies disappear from your unread notifications if someone else replies to them first. I don't know why that is, but it's been an issue for a while. This really bites you in the ass if hexreplybot is replying to you because you posted a YouTube link or something.
Same goes for me. There have been months-old replies that I only happened to see when looking through past threads I posted in. A couple times I felt really guilty because it was something I would have responded to, and then was like "should I reply now and come across as a total weirdo by responding months later, or just let the person think I'm an ass for not answering their question?"
My notifications have for the past 4 years been unreliable lol. Replies will get stuck for days. Sometimes they won't trigger notifications/unread. Mark All Read will only work like 25% of the time and usually if I want to clear notifications I have to hit the button, go back to the homepage, navigate back to the Inbox, and hit the button again.
I've just succumbed to it. If Hexbear doesn't want me to reply to something, I won't....