We have a pretty strict retention schedule (3 days on direct chats, 7 days on group/space chats).
If a user misses a chat, and the retention kicks in, the blue dot stays. Going into the chat doesn't clear the blue dot, the user has to right-click and "Leave" the chat with the user.
I guess having the blue dot there might have value (it indicates that you missed something). But it should clear by going into the empty chat.