Deactivate dotScribe Library folders you do not want appearing in your active content, and reactivate them whenever you need them again. Deactivation changes what is active for you; it does not delete the Library content.
When a parent folder is deactivated, its content and child folders are removed from your active view together.
Confirm that the correct folder is active or deactivated, then sync again. If the result still does not match the Online Library, see Sync your Online Library and desktop app.