As far as I know there is no way to migrate existing Facebook comments which use fb:comments/xid over to the new fb:comments/href version. There are some StackOverflow topics ( How to migrate Facebook comments from using "URL" property to "HREF", http://facebook.stackoverflow.com/q/8487357/138526) which supports this interpretation.
Now Facebook says in their FBML documentation:
Starting June 1, 2012 FBML apps will no longer work as all FBML endpoints will be removed
According to the docs 'xid' is FBML, not XFBML. Does that mean all old comments will be gone forever?
I got an official response from Facebook (finally) and I thought I share it here: Even if the 'xid' parameter is not mentioned in the XFBML docs, it somehow part of XFBML. Adding 'migrated="1"' will make the deprecation warning go away.
Source: https://developers.facebook.com/bugs/244684962306617