First thing, that you should understand, M2E Pro version 3.x is a new extension. It has 100% new code source. We have completely re-implemented our extension to make it better, faster and more flexible.

So you should not update, but install M2e Pro version 3.x via Magento Connect Manager.

The License Key for version 2.x does not work for version 3.x. There’s instructions in the Configuration Wizard, where to obtain license key.

We have implemented Migration Tool from 2.x to 3.x in the Configuration Wizard, which will be available after installation.