Thank you for your interest in SQLCipher and for posting to the discussion forum.
SQLCipher 3.x has different encryption settings than SQLCipher 4.x, so you’ll need to migrate your database(s) to use these new encryption settings (or open them in compatibility mode) as outlined in this post: Upgrading to SQLCipher 4
SQLCipher should properly migrate all your tables and database data when performing the migration, so you shouldn’t need to drop your tables and re-create them onUpgrade like you’re doing unless that’s an application requirement.