The table structure has stayed the exact same for our jos_jfbconnect_user_map table. If the Joomla User ID's are the same from the 'old' site to the 'new' site, you should just be able to copy the rows from the old database to the new table. Sometimes when you upgrade/migrate though, the user IDs actually change. In that case, you'd need to determine what the new user ID is and update the user_map table to use the new Joomla User ID from the 2.5 site.
Additionally, if you merge the tables, and a user has switched their Facebook account or connected to a new Joomla user, that will overwrite their setting with the old account.
Conversely, if you have the "Automatically map user's by email" setting, if a user re-visits the site and clicks the Login With Facebook button, it should re-enter their user mapping for them (if they use the same email address on Facebook and your site). It's a good way to recreate some/most of the mappings, but obviously won't do everything perfectly.
Hope that gives you some ideas and helps get you going again. Normally, during a migration, you just move all of the jos_jfbconnect_xyz tables from the old site to the new one and install the J2.5 version of JFBConnect. Our extension will work just normal using the 'moved' tables.
Good luck, and let us know if there's anything else we can help with!
Thanks,
Alex