Konstantinos,
I'm not sure what method from 4.0.2 is being deprecated off-hand, and specifically, which feature your site would be using from that featureset. We are constantly improving JFBConnect and keeping up with changes from Facebook. v4.0.2 was released about 10 months ago and there have been many compatibility improvements over that time. Our suggestion is to upgrade to the latest version. We haven't heard from any users reporting an email like that running the latest version, but if some feature we use does become deprecated, we'll have a work around available in the next release.
Hope that helps,
Alex