Scrivener has a mode called "corkboard" that makes this really easy. In corkboard view, Scrivener lays out an image of each scene as a sort of 3"x5" note card stuck to a real cork board, like this:
|Scrivener for Linux. Looks and works basically the same as the Windows version.|
As you can see, each scene is labeled at the top based simply on the document name - for simplicity's sake, I just call them "scene 1", "scene 2", etc. If I move them around, I just rename them so they stay in numeric order. In addition, you can set a label and status on each document: I have consistently labeled them as a "scene" (thus the dark mauve tab in the upper right corner) and given them a status of First Draft, which is shown as watermark text.
I have spent the last week going through each chapter in corkboard view like this, and adding my little notes to each card. Scrivener does not add those notes by itself, you need to do that. But having added them, I can now view a single chapter as a series of cards like this, each one with a little note telling me what the scene is about. How cool is that? I've seen how movies are often laid out ahead of time just like this, with note cards stuck to a board, one for each scene, but I have never heard of a novelist writing their story in this way. In my case, I wrote the novel first, and have now gone back to lay it all out in notecard form. In retrospect, I probably would have benefited from laying out the Balfrith story ahead of time like this, defining each scene, before ever writing it. But hey, I'm new to Scrivener and new to some of the tools available to me that might make the job of writing a bit easier and more efficient.
Now, back to the story. As I mentioned, I spent the last week laying out each chapter in corkboard view and then adding notes to each scene. Of course, that required me to speed-read each scene in order to remind myself what it was about, and then summarize the scene in a few words. That alone provided great benefit in helping me to review the overall story.
And now, having done this ground-work, I can move to the next step, which is to review each chapter and scene at a high level and decide whether any scenes need to be shifted around, or added, or deleted, or whether anything else should be changed at a rough-draft level as I finalize the overall story and its structure.
The completion of this phase will probably take a while. I have already noted that the story is missing several scenes which will need to be written, as well as some existing scenes needing significant changes to make them "work". There are even a few I have tagged as possibly superfluous. I will wait until I've done some of the other revision work before I decide whether to actually delete them.
My goal is to finish this first round of revisions by the end of the year. Maybe I'll be able to get it done more quickly than that, but my work and travel schedule is going to be fairly busy for the next few months, so I'm anticipating not having a lot of time to work on the story. I think my year-end goal is reasonable, but only time will tell.