I can probably help you figure this out.
Couple of things, what version did you upgrade from? Did you complete the database upgrade when you installed? Before or after you upgraded were you doing anything special related to the users WPeC created in the prior releases?
Something related to the fix in 3.8.14 and 126.96.36.199 that stops WPeC from using the users table for transient user data like ( cart data ) might be a place to look for a possible reason for the missing user records. The upgrade process tries to delete all of the WPeC anonymous users that accumulated. Because there can be ten's of thousands of these the processes is done slowly over a period of time.
If the users are indeed gone, to get the users back you will need to use the database backup you did immediately before the upgrade. The WordPress users table and the user meta table will need to be restored.
You can manually create an admin user using a tool like phpMyAdmin.