Upgrading JFBConnect won't affect your current users. Each time you install JFBConnect, the installation process will do any updates to the database and files that are necessary but will not alter or remove any users you already have.
We and all our customers have tested the upgrade process pretty thoroughly and we haven't heard of any issues during the upgrade process with users losing their connections.
I hope that helps, but should you run into any issues, please let us know.
Thanks,
Alex