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 topic
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