Thanks for the update.
Right, hence the iCloud-level quality I referred to. Status that doesn’t seem to work right, sync that can take minutes or longer to start, etc. It used to be iCloud was clearly worse than everything, but now everything feels a bit like it does, and even iCloud seems appealing to some, I’ve noticed (all according to plan, I’m sure).
It’s something we’ll have to keep an eye on in our support involving sync. Just to double check, did you ever get around to resetting the Dropbox cache? That can often clear up “jams” like this.
Otherwise, there are alternatives, such as Maestral, that sync your content in a more straight-forward manner. No weird proxy folders that seemingly only exist in the Finder sidebar, no “smart sync” that removes all your data from the disk and makes your own local backups worthless, no greedy policies that only allow you to keep one single folder “offline” at a time (that this word should even be used with a sync service is indicative of how lost these companies have become as to their original purpose), or only install on three devices. It does use the Dropbox API, like Scrivener itself does, so it will be slower than you are accustomed to. They throttle that connection to cripple developers like this, who come along and make demonstrably better clients than they do. 
It would be so very nice if I weren’t relegated to those two choices, if I could instead have Scrivener for iPad treat external .scriv files in a way similar to what the desktop app offers — opening the file opens the app, editing happens, it’s saved without needing to import or export, etc. — though I imagine the coding might be fraught, as iOS in general really isn’t designed to work that way.
It’s getting… better. Sort of. At least so long as you don’t edit packages (which Scrivener needs to) over cloud accounts. iOS still struggles with the concept that one program might upload more than one file at a time, at least in my testing. But they are at least working on fixing past mistakes.
We’re so close to having an alternative, though, as I’m able to import existing .scriv projects from my iCloud drive into Scrivener for iPad.
I guess you could think of it that way, as importing and exporting, but if you go into Files.app you’ll see it’s just copying things around on the file system. This is the only way I work in fact, and honestly would probably do so even if I could do the above. I would always prefer the safer path when it comes to sync. I think of the tech more as a thumb drive replacement, not a file server replacement.