1.) Update to ReadCube Pro - you can make sure this process is complete by checking the "About ReadCube" button and making sure you're using a 2.0 version.
2.) Go into your preferences menu and under the "ReadCube Pro" tab, make sure sync is enabled.
3.) Manually hit the sync button in your library and make sure it finishes.
4.) You can now reformat safely. When you finish, just install ReadCube Pro, once more enable syncing, and hit that sync button. Your library will come back.