Hi Brian.
The s2Member Pro update will never happen automatically. And I don’t know if you have something on your installation that would update the s2Member Framework automatically. This is not something s2Member forces or has a way to do even. These updates are normally started by the administrator.
From what you’re saying, it sounds like some automated task on your site updated the s2Member Framework, but that didn’t update the Pro add-on because it’s an add-on not a plugin, and so the Pro features got disabled because Framework and Pro versions need to match for Pro to be active.
Maybe you activated automatic plugin updates, or perhaps your webhost did. I don’t know, but this is something particular to your site. It’s not something s2Member can prevent if you have it setup like that. You’d need to adjust the configuration to skip s2Member from the automated updates.
I look forward to your update.