You can do user and system configuration backup using the "backup now" option. It is possible via GUI.
http://www.cisco.com/en/US/docs/net_mgmt/cisco_secure_access_control_server_for_windows/4.1/user/SCBasic.html#wp222516
If you use an encrypted backup file to restore ACS data, you must provide the exact password that you entered in the Encryption Password box when the backup was created.
You have to reimaged the appliance using ACS 4.2 recovery CD as it runs on 2003. Once you will be able to reiamge it, you can restore the database taken in previous step. In the below listed link step 5 and step 7 are very important.
Step 5 To restore user and group database information, check the User and Group Database check box.
Step 7 To upgrade to ACS 4.2 using the ACS 4.1 backup file check the Restore from 4.1 backup file to ACS 4.2 check box. You use this option to upgrade to ACS 4.2 using the ACS 4.1 backup file. The upgrade functionality is then implemented, and the user and group databases and the system configuration will be restored.
Manually restore backup
http://www.cisco.com/en/US/docs/net_mgmt/cisco_secure_access_control_server_for_windows/4.2/user/guide/SCBasic.html#wp222758
Jatin Katyal
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~Jatin