First, I don’t understand why you say the folders are empty. Each one has a scene file nested inside.
Sorry, that wasn’t clear, I meant the folder itself has no text content—if you were to select it and turn corkboard/outliner/scrivenings mode off, the text editor for it would be empty—here is where you could put an epigraph or even chapter notes that don’t print. Thus all the folder is providing is its name, like “Chapter Twelve”, which you get automatically added anyway from the compile settings.
Why wouldn’t the foundational principle remain the same: folder contains the scene file. Scrivener should format the same whether I have one scene file or three in any given folder.
To make that kind of arrangement work best for what you want, you’d probably want to disable Include in Compile for all of the folders, using the Inspector, and just let the files operate on their own in a similar manner to the checklist I already provided. The folders at that point would be purely cosmetic—you could even use more descriptive names for the folders that make sense for story tracking, since nobody is ever going to see them anyway.
I’d argue that chapter folders are for more than just organizing lots of elements. For one, removing the files completely means I am left with a string of scene files titled w/ the POV of that chapter. Only now I have a hard time clicking around my own manuscript because I can no longer see the chapter numbers.
Well all right, if it works better for you that way, you could try the above suggestion instead. But to me it seems there would be better ways to handle what you’re describing: like clicking on Draft, and switching
View ▸ Corkboard Options ▸ Show Card Numbers and/or
View ▸ Outliner Options ▸ Title with Numbers. That way you get the numbering you want—and it actually reflects the order of things rather than being typed in text. If a chapter gets inserted, you don’t have to go in and rename everything below it.
When I’m ready to format the book for publishing in Vellum, the software compiles all those flat scene files into one single chapter. The folders are crucial for making Vellum understand the chapter structure.
The only thing that determines where a chapter break is is the Section Layout you use for the things that should be chapters. They aren’t a flat list of scenes at that point, they are a flat list of chapters. The software itself doesn’t have any programming that says folders are chapters, that is 100% a matter of how you set things up.
Case in point, if you still have the template help file in your binder (with the blue info icon at the very top), then search that file for the phrase, “Working with chapters instead of scenes”. It goes provide a checklist similar to the one I provided above.
But like I say, if you find this better, it’s not the end of the world to work that way, but it’s going to be hard to split the chapter break between two different elements of the outline like you’re trying to do, no matter.