So far Hall of Famer has always (recently) made a way to upgrade your site without losing any of your data, I would assume that v1.4.0 would work the same way. From my understanding a lot of the base script will be radically different, so highly customized sites will most likely not be upgradeable with an upgrade script. I'm sure that he will post a guide to manually update the sites as well.
All of your users and data are saved in the database of your host server, so changing the script on the website doesn't edit any of these tables, but the tables may change. He mentioned in his last update thread that he will post a guide on how to migrate all of your data, so we should be safe.
It will take some work but we should be safe.
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