You will have identical groups and references when Sync completes processing.
If you make any changes to references or file attachments, when you synchronise the libraries these changes will be carried across so that each library matches the other. This includes updates and additions to groups in both libraries. This also means that if you delete a reference from either your desktop or online library and then sync your libraries, the reference will be deleted in both places.
It is advisable to create a compressed library for backup before you begin the sync process. Go to the File menu and select Compressed Library.
To synchronise your library:
Sync settings are editable within EndNote Desktop:
You can change your email address or password and also choose whether to sync automatically.