We just upgraded to the new version and all of our 20 or so custom fields are missing. Completely gone even in the database. This is the second time with S2 that we have had to recreate custom fields and our client is NOT happy. Even all the Authorize.net settings disappeared. This has not happened with other plugins such as Event Espresso.
Not the case. The safeguards are on. The site was moved to a new server, the database was repopulated. Same domain but the URL was changed from https to http. All other plugins were reactivated with no loss of data.
I am not sure, but I think the custom fields disappeared with the update. Now wondering if I should apply the new update.
I see, that's very odd. You should update the plugin, but I suggest making a backup first.
With s2Member Pro now you can also export the s2Member options to import them back if needed, which would include the custom registration fields. WP Admin -> s2Member -> Import/Export -> Options