When you change your URL structure, Facebook can 'reset' your site on their whitelist. Basically, they want to know if your content is good (not malicious, spammy, etc). They do this by building up reputation for your content as they see more and more of it and eventually just trust everything. If all of a sudden they can't access your old content, or it's changed a lot, then that process may start over. It should only take a day or so for them to see the new URLs and get you back to where you were though. Using the Debug Tool just forces the refresh of their cache for those specific pages and helps move things along quicker.
As for getting back the Like's / Comments from the old URLs, the only way to do that is to replace the Like or Comment button with a manual {JFBCLike url=http://xyz/index.php?...} or {JFBCComments url=http://xyz/index.php?...} tag that points to the 'old' URL. All social interactions are stored by the URL they were made on, so if you change all the URLs the content with those are still 'in' Facebook, but not shown since the 'new' URL is shown.
JFBConnect does let you set what Joomla article IDs should be excluded from the automatic Like/Comment stuff, so you'd need to specify all your old content that you want to preserve, then add the buttons yourself to just that content. Then, JFBConnect will add the widgets to all new content with the new URLs automatically.
Hope that makes sense. It's not an easy process, we'll agree, but changing your URL structure has an impact on SEO, user navigation and a lot of other things as well. Social integration is another affect that we simply can't just get around.
Thanks,
Alex
FB Like button stop working after enable friently URL & rewrite
