Likes and Comments are associated with a URL. When you update that URL, even from http to https, the Like's remain with the 'old' URL. You can't re-associate those Like's with the new URL. However, in the JFBConnect -> Configuration area, we have a 'Force Scheme' option which can be used to force all Like buttons to use http or https. If you set that to http, then all your Like buttons will go back to using http. The problem with that is:
* When shared to Facebook, the links will be http. Please make sure you have https setup
* All future content will still use http links, so even though that content will never have lived on http, it will show up that way
I hope that helps explain,
Alex