A method and system for generating a patch file from an old version of data which consists of a series of elements and a new version of data which also consists of a series of elements. Several patch files may then be aggregated into a secure, portable compressed archive to decrease the storage and transfer requirements of the patch file. The compressed archive uses an encryption process and may include an authentication process using digital signatures to secure the contents of the patch file from unauthorized access and to validate the identity of the creator of the archive. The archive is preferably in the format of a self-extracting .ZIP file, which file may include a rules-based form of intelligence to detect the presence of the appropriate files to be patched and to determine how the patching process should proceed.