I think the issue is that QueryHierarchy.Save() isn't called at the end of import process. Without that it still appears while the instance/session of the Project Manager is open. As soon as the instance is closed those changes are discarded as since the Save is never called and therefore TFS doesn't fire the changed event.
I found this digging through the code of https://wiqadmin.codeplex.com/
I found this digging through the code of https://wiqadmin.codeplex.com/