I’m not entirely clear on your meaning, so I’ll explain two scenarios and maybe one will answer what you want. Otherwise, feel free to correct me!
First, if what you mean is that you have empty documents showing in the binder, because you’ve deleted all the text from them, and you want to get rid of those empty documents (your original “chapter” documents, now perhaps serving no purpose?), you can simply select them in the binder and then use cmd-delete to move them to the trash (or hit the “Trash” icon in the toolbar). Project>Empty Trash (or a right click in the binder and choosing Empty Trash there) will delete the documents permanently; until you empty the trash, you can always drag them out of the trash to restore them if you wish.
Second, if you want to retain these chapter documents in the structure–for instance, if you have your novel broken up into different chapter folders, each empty but with a set of subdocument scenes–but you don’t like the blank space showing up when you view your draft in Scrivenings mode, you can remove them in a few ways. First is just to select all in the draft and then cmd-click to deselect the empty documents that you don’t want to appear. That will work but will require you to redo it every time you want to view the whole draft this way.
A better method would be to create a collection of all the scenes so that you can quickly just view them all together. You could this by selecting the draft-minus-empty-docs as above, clicking the “Collections” icon in the toolbar, and then clicking the + sign that appears at the top of the binder to the right of the word “Collections”. This will create a new collection and add your selected documents to it. You can name it whatever you wish by clicking on “New Collection” in the tab and can switch back to the regular binder by clicking the “Binder” tab toward the top of the binder or the “x” in the binder footer.
You could also make a dynamic collection by searching for a common feature unique to your scene documents–for instance, if all your scenes are labeled “scene” and your empty chapter documents are labeled “chapter,” you could type “scene” in the search bar, choose in the dropdown to search in “label” and in Draft only, and then at the bottom of that menu choose “Save search.” At the moment this will look just like the static collection you’d get following the other method, but it means that if you add new documents to the binder and label them “scene,” they’ll automatically be added (and in the proper position); likewise, if you change the label on a current scene, turning it into “notes” or what have you, it will be removed from the collection.
In either case, you can then view the collection in Scrivenings mode and it will not include the blank documents, so your scenes will run smoothly one after the other.
Does any of that help what you’re really after?