The invention is a method of transferring user data from a first instance of a package to a second instance of another package corresponding to an upgraded version. The first instance stores the user data in its own storage format. The two instances are embedded in a secure element. The method comprises the steps of: establishing a direct channel within the portable secure device between the two instances, the first instance gets in a locked state where it refuses any service requests except the communication with the second instance, prepares a pack by formatting the user data in a transport format, and automatically sends the pack to the second instance through the direct channel, the second instance retrieves the user data from the pack and stores the user data in another storage format.