It finally resolved itself today, but this behavior happened four times yesterday.
I had created a new doc for a new scene at the end of a chapter (folder) in the iOS version, did some writing, closed the project, synced with Dropbox. Opened in Windows, did some more writing, and also decided to move the scene to the beginning of the chapter (folder). Saved, synced with Dropbox.
Synced iOS and Dropbox and opened project. All the text changes I made in Windows had accurately saved and synced, but the document was moved back to the end of the chapter (final doc in the folder). Typed some more, saved/synced, closed.
Opened the project back in Windows, and because I had now saved and synced in iOS, the doc was also at the end again in Windows. Moved the doc back to the front. Also swapped the location of two chapters (folders). Saved and synced.
Synced on iOS again, and, again, the text changes were kept, but it once again moved the doc to the end and also the folders were in their original positions instead of being swapped as they were supposed to be.
This kept happening repeatedly all day yesterday. All the content changes were syncing, but on iOS for whatever reason binder organization was not syncing correctly.
What seemed to work was today after I made changes in Windows, I wanted much longer to open and sync in iOS. I don’t know if it was just a weird hiccup and there is no bug, or if there is a bug, or if there is a caching issue, or what, but it was getting very annoying yesterday.
As I said, it has since resolved itself, but I just wanted to post this in case anyone else has had the problem and or start a history for the developers if it comes up for other users later.