I must really have explained it poorly. The unintuitive part is when I search for a folder and select it using "Goto Anything" with @foldername, I jump to it, so I don't see where I am in the tree. The folder shows up empty, in the notes panel, however, it's not empty, it contains sub-folders with lots of notes.
In order to find the sub-folders and those notes, I still have to go back to the notebook list and manually find the notebook.
The other way this could be solved I suppose, is that when I search and select the notebook, the notebook tree jumps to the location. Now that I think about it, this may be the best way to fix this and I'll make a separate thread about this