comments have disappeared

Damiaan,
Comments are associated with a specific URL on your site. If you're using the JFBCComments module or {JFBCComments} tag, it's highly recommend that you specify the href parameter so that that box is 'locked' to a URL. If you don't, the comment box will be attached to whatever URL the page is currently on. Unfortunately, Joomla usually has multiple ways to hit the same page:
site.com/index.php?option=com_content&view=article&id=12
site.com/index.php?option=com_content&vi...icle&id=12&Itemid=15
site.com/link-to-article.html
www.site.com/link-to-article.html

If a user comments on each of these pages, they will all be 'unique' comments and not associated with each other, even if all the pages load the same content.

Our Content Plugin gets around this pretty well by always trying to use the canonical URL (best, final destination) for the page. If you're simply adding comment boxes to Joomla (or K2) article pages, we'd highly recommend you move to the Content plugin instead, as it should minimize these types of issues. Alternatively, if you're using a 3rd party SEF extension, many of them have settings to always redirect users to the 'best' SEF URL, if they aren't already on it. Joomla, unfortunately, doesn't do this.

Hope that all makes sense. It can get confusing, so if you have any other questions, just let us know!
Alex

Damiaan,
Unfortunately, no, there's no way to either:
1) Let Facebook know about a new URL to associate old comments with - Man, we'd love that.
2) Have sh404SEF redirect to the 'old' URL.

We do recommend enabling the following settings in sh404SEF, which will help to ensure that the same URL is always used regardless of how the user reaches the page:
301 redirect from JOOMLA SEF to sh404SEF
301 redirect from non-sef to sef URL
Also, if you don't redirect from www to non-www (or the opposite) in your .htacess file or elsewhere, I'd let sh404SEF take care of that too.

Hope that all helps, but if you have any other questions, you know where to find us

Finally, please consider leaving a rating and review on the Joomla Extension Directory for JFBConnect, or our support. It's certainly not required, but very appreciated!
extensions.joomla.org/extensions/social-...ook-integration/7215

Good luck,
Alex