The process of upgrading to Release 6 is new and is different from the previous upgrading process. Beginning with Release 6, you no longer perform an in-place installation. Instead, install Java CAPS 6 in a new directory, and then import your Projects from previous releases.
When upgrading from previous releases of Java CAPS to release 6:
Install Java CAPS in a new directory.
Export your Projects and Environments from the earlier release of Java CAPS
Import your Projects and Environments into release 6 using the NetBeans IDE Update Center
For instructions on how to complete a successful upgrade see Upgrading to Java CAPS 6.