At the moment, iCloud for Windows is not an option for syncing Scrivener projects.
On Windows, a Scrivener project is in the form of a folder with a .scriv extension, and everything within this folder is a necessary component of your project. Currently, iCloud for Windows is incapable of copying the contents of a .scriv folder, so users attempting to sync a project between devices using this service will find themselves with an empty container rather than a whole project.
While you can still use iCloud to sync a Scrivener project between Mac computers, iCloud syncing cross-platform or between Windows computers is not advised.
This advice applies only to live Scrivener projects. If you are using iCloud for Windows to store and sync backup copies of your projects in ZIP file format, you may continue to do so.
We would encourage everyone encountering this issue to send their feedback to Apple to have it investigated further.