http://www.olimex.com/dev/avr-jtag-upgrade.html
We put on above page instructions how to upgrade your old firmware (pre 4.08) to the current one version of AVR Studio.
So far AVR-JTAG upgrade is not so simple, but we are working on Upgrade.exe which will do all things written on the web page automatically and there will be no need for external programmer AVR-PGxB to make the upgrade.
For some reasons Atmel didn’t disclosed firmware upgrade command syntax in AVR-JTAG protocol, which delay the release of the simple solution, anyway the above described procedure works reliable.
Best regards
Tsvetan