Hello luckman212,
Before the recent OpenVPN Connect v3 release, it would not be easily possible to migrate from Connect v2 to Connect v3. That is because these are separate programs and they can live side-by-side on the same system, and their configurations are kept separate. So upgrading from Connect v2 to v3 will simply not pick up such configuration.
However, OpenVPN Connect v3.3 for Windows adds a command line interface. You could automate importing the necessary profiles with a deployment tool, and automate the uninstallation of Connect v2 as well. The command line parameters can be found here:
https://openvpn.net/vpn-server-resources/command-line-functionality-for-openvpn-connect/
And of course another option is that people can simply go to your Access Server web interface and download and install the Connect v3 client and have it already preconfigured for use for them and simply ignore or remove Connect v2 entirely.
last minute edit: we do have in our roadmap to add a function to do an automatic migration from connect v2 to v3 but that currently is not yet available.
Kind regards,
Johan