I am afraid that Bitnami Open edX Stack change dramatically from previous versions to Ecualyptus. The previous structure differed from the official Open edX structure and we took the hard decision to change it in order to adapt it the official documentation and make it more user friendly. Therefore there is not an easy way to upgrade older versions to the current one.
You can try to export your courses and launch a new server with the new version and import them. We plan to create a section in the documentation explaining how to upgrade from edX Eucalyptus to Ficus and further versions so it would be easy to move to the latest version in the future.