Once you have imported all previous Projects and Environment into Java CAPS 6.2 or have updated the previous Repository, you need to redeploy and in some cases reconfigure the Projects. Runtime components need to be recreated as well.
Complete the steps under Upgrading the Repository.
Recreate any runtime artifacts using the GlassFish Admin Console for Java CAPS 6.2.
This could include any connection pools, security attributes, application configurations, application variables, and so on.
Reinstall the required plugins in Enterprise Manager.
Open any JBI Projects in NetBeans Project window.
Build and deploy all Repository and JBI Projects to the new GlassFish server installed with Java CAPS 6.2.