I was AFK almost a week, and wanted to catch up on my backlog (half is probably @Boukert, but whatever). Anyways, I refreshed today without ever clicking my mailbox, and suddenly half my notification number is gone. I did not visit my notification tab at all, and it was literally halved. I like to get back to people, even if it was after 5 or so days of inactivity...I don't check my messages until I know I have time to do enough so I don't forget.
Aka I loved the "Mark as read" for all comment/submission replies thing, that you removed.
Anyways, never clicked the mailbox, and suddenly I went from 29 notifications to 15. I can file a bug, but I'd rather bitch here first.
You want us to investigate @polsaker ?