To upgrade a 0.3.x system to 0.4.x you have to make sure your system is using 0.3.7.1. If not, use the WebGUI update management or the following CLI command:
apt-get update
apt-get upgrade
After that you can upgrade your system to 0.4.x using the following command:
omv-release-upgrade
Please make sure that there are 0.4.x versions of your installed plugins available before upgrading the system.