Domino 4.4+ introduced resumable workspaces. This means files will persist in your workspace once saved and will be there once the workspace is restarted. However, in prior versions of Domino these changes would then automatically sync when the workspace stops.
Users must now manually sync files prior to stopping a workspace to have those changes show in the project file list in the Domino UI. When stopping a resumable workspace in Domino 4.4+ you will not be prompted to sync, so if you need your updates saved for another user sharing the project, sync prior to stopping the workspace.