AS/400 Tips 17

Retaining Customization
It is often required or desirable to customize certain system attributes from how they are set out of the box. For example, you may want to change certain command defaults from the IBM-shipped defaults.
When you do an O/S upgrade however, you'll find that your changes were erased. Unless you kept very good documentation, you'll be hard pressed to remember which changes you made.
A good workaround to this is to create a CL source member that contains all the commands you've customized your system with. Keep the source member up to date and include thorough comments.Compile this member into a program, and simply run the program whenever you've done an upgrade.

Source: http://midwareservices.com/tipstricks/windows.htm