When I have a chat in a separated window, the original icon in the Conversations window will flash for every message no matter if it's read or unread.
To reproduce:
1) Have an active chat going (for example by IMing somebody)
2) Open the Conversations window
3) Click the "Move this conversation to a separate window" button
4) Tab into the text input field of the new chat window
5) Receive an IM. Since this conversation is your active window, you've read this message.
6) You will see that the original icon in the Conversation window flashes even though.
Also, when you receive an IM while the separated window is currently not your active window, tabbing back into it will not remove the flashing of the original icon in the Conversations list.
My specific use case is the "Nearby chat" icon. I have the Nearby Chat in a separated window since it had been like that in the old days and I'm used to it. The constantly flashing "Nearby chat" icon in the conversations list drives me crazy. I wish there was no icon at all. Maybe you could remove every icon that belongs to a separated window if this feature request ever gets implemented https://feedback.secondlife.com/feature-requests/p/show-im-status-icons