Live SDK 5.6 is out now, but none of the code or API references have been removed. This ensures backwards compatibility with existing code written for previous versions of Live SDK. This includes the API paths, which will continue to include the term skydrive.
The store approval process is flagging UI references to Skydrive. If you have strings that are visible to the user that reference Skydrive you should replace them with references to OneDrive and resubmit your app.