“I’m doing the thing that L&L has all along told us not to do because it will cause problems, but this means the program shouldn’t exist.”
I know that changing one’s process is painful and difficult, but seriously, point me to any non-trivial application that synchronizes discrete files using third-party sync engines (that is, not custom sync logic or database replication) that allows you to keep files open on one or more of the synchronizing systems 100% of the time without causing issues along the way.
To be precise, if you – accidentally or deliberately – find that the Mac project was open while changes were made to the iOS project, then you MUST explicitly incorporate those changes via the File -> Sync -> With Mobile Devices command. That command ensures that the files loaded into local memory – which are under Scrivener’s control – match the files on the hard disk, which may have been changed by Dropbox.
If you don’t do this every single time, you are very likely to encounter synchronization conflicts, and there’s a better than 50-50 chance that you’ll lose work.
I don’t know about you, but I’m not that good. It’s easier to just shut Mac Scrivener down when I’m not using it.
iOS Scrivener puts its changes in a special “Mobile” folder within the project. Mac (or Windows) Scrivener then reviews those changes for potential sync conflicts, then incorporates the changed files into the main project structure.
So, if changes are made to the project via iOS Scrivener, and the project is opened and then closed on the Mac, that incorporation step will occur and the Mac version of the project will change as a result.