That may be an unrelated issue. This issue is only about folders staying in the tree when deleted, probably only happening when they are the active folder/tab in at least one window.
For your issue, please see the Changes to folders are not always detected FAQ. If you want to, please create a separate thread for your problem and provide the debub information that the FAQ talks about + any other details about what might be special about the folder where you're seeing it vs other folders.