Yep.
As SkyeFire said, there is no synchronization
But You can change programs and other files in Configuration Workspace, and when You deploy the project, everything will be loaded on the robot controller.
As a rule of thumb, You can use Programming workspace when in need to change specific config files or programs, and use Configuration workspace when doing major changes in the system.
Remember that project deployment requires a robot reconfiguration, what will probably shut down robot safety and so on, while Programming workspace (and, specifically a feature called WorkOnline) doesn't need it, being a smooth process.