Syncing Scrivener Projects to the Cloud
When you're working with any Scrivener project that syncs to the cloud, you must close it on one computer or device before you open it on another. If not, you'll get a warning from Scrivener that the project may be open on another computer. Always make sure that you've closed the project first, or you may lose data. If not, Scrivener will warn you of potential conflicts. (See the Scrivener manual, section 14.2.2 for more on resolving conflicts.)
When shutting down a project, especially a large project with lots of research files, don't shut down your computer or put it to sleep until your sure the project has been uploaded to the cloud. If you don't wait, it may only partially sync, and, if you then open it on another computer, you may lose data.
The same is the case when you open or start up your other computer. Give the cloud service enough time to download the project to make sure you have all of its elements. Opening your project too soon could lead to data loss.