SQLite supports encryption integration, but the default open source SQLite distribution does not support encryption. Encrypted versions of SQLite will only migrate for different clients or tools if they all use the same encryption extension.
SQLite developers themselves are distributing a commercial version of SQLite that transparently supports encryption. When this module is used for encryption, encryption works on different platforms, and each byte written to the file is encrypted. There is nothing in the encrypted SQLite file stored on disk to indicate its SQLite database. Many tools support this implementation, allowing you to instead download the commercial sqlite.dll file instead of open source.
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http://probertson.com/articles/2008/11/18/air-1_5-encrypted-sqlite-database-how-to/