New Thunderbird versions has this annoying feature of threading your Emails when they are part of a 'coversation'. However, when a new Email comes it disappears and does not highlight threads with new Emails so you have to hunt for it. The solution for this is listed here: Source 5y
Note: to access Thunderbird config you have to go to Tools > Settings > use the search for "Config editor".
More opinions appreciated on thunderbird annoying threaded display should be expanded briskly how what the big picture forms.