Lisa,
JFBConnect fully supports the July migration already. If you re-run Autotune, it will automatically enable that migration setting for you.
The href note is simply stating that if you use a Like button that points to a different page, you must use the full URL (ex.
yoursite.com/link-to-page) instead of a relative URL, which Facebook used to support (ex. /link-to-page).
JFBConnect automatically generates an absolute URL when using our Like button. The only way you'd be in violation of the migration is if you implemented the JFBCLike tag or module and specifically used a relative URL, like {JFBCLike href=/link-to-your-page} That's generally not common and not something we've ever recommended.
As always though, you can enable the migration, test your Like buttons, and if you run into issues, disable the migration. That's the purpose of the migrations.. so that you can test before the are enabled for everyon. (in July)
Hope that helps,
Alex