I've been helping someone diagnose a technical issue through Lemmy PM's the last month or so, and have accumulated a lot of messages back and forth. (Around 130 I'd say.)
When I get a new message, the total number of messages that I've received shows as a notification for a while, until it eventually disappears. (I haven't fully tested it but I think it disappears on reboot once I've replied.) Receiving comment replies or a new pm brings the notification back.
The screenshot shows what I see when filtering for unread messages. Thus, there are no unread messages, let alone 130 of them.
The entire conversation has been had in the same message thread. Not sure if this is a Lemmy issue or boost issue.
I've been having the same issue for a while too. Like someone else mentioned, logging into the web browser and clearing them there works for me... until the next message I receive.