I would say that in most cases Collections are not the best tool for this job, because they are intentionally limited to flat lists. They are much better when working in smaller scopes, like say the section order in a chapter that has no further nesting beneath it—at least for this use of them, there are of course many other good uses for having a flat list of things pulled from all over the binder.
But for a highly or even moderately structured rethinking that encompasses most or all of the Draft folder—you really want another outline for that. The simplest approach there is to simply duplicate the entire Draft folder and set it aside at the top level in the binder. Now you are free to do whatever you want in the Draft folder. If the experiment ends up not working out you can trash it all and restore the original back into the Draft. There is little overhead in doing this unless you embed a lot of graphics in the text, and the only major downside is that search results can get a bit cluttered—but that can be easily mitigated by using the project search option to limit the results to the Draft folder.
Here are a couple threads with existing reading material around this topic:
- Misc tips and how to preserve just the structure of the draft outline. In some cases, if you’re pretty sure you won’t revert, just having a linked and indented list of titles in a single document as a reference of how things were is good enough. You can click through it and use it as a kind of ToC, so it is handy in that regard as well.
- More on collections: although as I say I don’t think this is your best tool here, this goes into how you can integrate collections more seamlessly in the project window and such, and you might find it useful, particularly if you approach collections as described above, as a smaller scale tool that you use to work on one area, implement it into the draft order once happy with it, then move on to the next area.