As I understand it, you can arrange items in a collection exactly as you wish, without altering their position in the Binder. So you can reorder items according to your preferences, which I suppose is why you don’t get the original hierarchy?
What you can do is use the ‘Reveal in Binder’ command to see where they actually are.
This is where a dual pane system would be fantastic in Scrivener - in one pane you could see the items in a Collection, in the other you could see the Binder, or another Collection, etc. That would make it much easier to compare the locations of documents in Collection compared with their location in the Binder. Perhaps there is already a way to do this? If so, I’m afraid I don’t know it.
I’m not sure if we’re talking about the same thing, but I just tried a split view with something from the Binder in one pane, and something from a Collection in the other - clicking the header bar of either changed focus to that pane, but it didn’t show any difference in the Sidebar.
For example, if the focus is on the pane with a Collection item and the Sidebar also shows the Collection … then I click on the header bar of the document in the other pane (not in the Collection), the Sidebar doesn’t change, it still shows the Collection.
I think what I was suggesting was a true ‘dual browser’ view, where you get not only a view of two different documents, but also two different sidebars, each showing the location of that particular document and how it was navigated to (i.e. Binder, Search, or Collection).
What I meant was that if you first choose a vertical split, click the topmost level in the Binder so it is shown in one of the splits, select Outline view, click the document symbol to the left of the title in the title bar at the top of that split and choose ‘Lock in place’, then you will essentially have a “binder” available all the time in that split. It won’t change if you click in the binder or choose a collection or what ever, but you can expand and collapse branches in the outline if you want to.
You can then swap to the other split in the editor and show something from the collection in there, as scrivenings or cork board. In the binder pane you can view the Binder or a Collection or the Search result, but the Outline in the locked editor pane won’t change.