sorry for the late reply!
Updating Boxcryptor should definitively not disable pin / password protection.
If you updated from a very old version, it is possible that Boxcryptor reset its user settings, and you were faced with the initial sign-in screen.
Then, on consecutive Boxcryptor starts, since the app reset and has no App Protection enabled by default, you would notice the missing pin/password screen.
If this reproducible happens on every update, please write us at firstname.lastname@example.org.