After you have migrated your applications, you need to migrate your instance configurations.
Migration of WebSphere Application Server Version 3.5 Standard Edition to WebSphere Application Server - Express requires a product level of Version 3.5.6 or later.
See Migration prerequisites to determine the currently installed product level of WebSphere Application Server Version 3.5.
Migrate to a new WebSphere Application Server - Express instance
This topic contains detailed information and step-by-step instructions for migrating a WebSphere Application Server Version 3.5.6 (or later) instance to a new WebSphere Application Server - Express instance.