I am running the latest version of Scrivener on my iPhone, iPad and Desktop (Windows.)
I have constant sync issues with a few projects. They’ve never been opened on multiple devices at once, I never see the error on my iPad or iPhone, just on the desktop. Is there some file that is buried in the bundle that is causing this that I can delete?
The story currently has around 50K words, plus character sheets, settings, and a metric crap ton of research…
Make sure that Dropbox is fully synchronized from the iOS device to the Dropbox server and from the server to the desktop before opening projects on the desktop. This is a two step process, and takes a measurable amount of time. (Depending on your connection speed, plus Dropbox itself has a bit of overhead.) Similarly, make sure that Dropbox has fully synchronized from the desktop to the server before sleeping or shutting down the computer.
Also, make sure that Dropbox on the desktop is configured for local storage of all Scrivener projects. Allowing online-only storage is more or less guaranteed to cause a variety of issues.
If Scrivener reports a synchronization error, be sure to fix it promptly. It will not go away if ignored.
If none of these tips helps, could you tell us more about your work habits? For instance, if you often work at a coffee shop, then close your computer abruptly and leave, you might find that Dropbox is failing to synchronize work done at the coffee shop.
Well, My desktop has stopped doing the constant pestering about a sync conflict.
My normal workflow is less working from anywhere but home (I will take my iPad and sit on the couch. Ipad is a Cellular/WiFi model so it’s always connected in some way. before I switch back to the desktop, I will back all the way out of the project, sync to Dropbox, wait for it to finish, and then, wake the desktop up, wait on it to sync, and once Dropbox has indicated that it is done, open the project.
Scrivener on my windows machine is set to auto quit after 30 minutes, which is less time than it will take me to get to somewhere else that I am going to write, and the system time for sleep is longer than time it would take to close Scrivener and upload to Dropbox.
Are you mentioning this because you leave your projects open in desktop Scrivener when you open them on the iPad?
If so, yes that’s supposed to work–that’s why the Sync with Mobile Device feature exists–but the only time I ever have a sync a issue is when I use this approach. A safer way is to close your project on the desktop before moving to the iPad.
ETA - Never mind! I just saw this in your original post, which answers my question. 
Best,
Jim