Hello Damian,
Just to clarify, these are 2 different programs, and they are not related to each other in the sense that OpenVPN Connect v3 is a continuation or newer version of OpenVPN GUI v2.6 or such. So if you're happy with OpenVPN GUI and want the latest version of that, that's at the moment bundled together with OpenVPN v2.6 for Windows.
Now if you want to switch to OpenVPN Connect, that's a different program. And it has a different approach. It's more aimed to be user-friendly and simple and to be bundled with the commercial products like Access Server and CloudConnexa, but retains compatibility with open source servers too. As one of the major differences, you can only have 1 active VPN tunnel at a time. But you can of course have multiple connection profiles that you can select from. So if this limitation is a problem for you, then you should stick to OpenVPN GUI which does support multiple simultaneous connections.
In OpenVPN Connect v3, if you want to import profiles, you'll need to use the 'import from file' option and select the profile you want to import. You can't just dump them in a directory. There is a command line guide that can explain how to automate this import process on the command line however, so if you have a lots of profiles to import, then it can be automated.
If a connection profile does not have a client certificate, then that needs to be either provided by having it in the certificate store, or if the connection profile can operate entirely without a client certificate (which is rare but we've seen this weird type of configuration), it needs to be adjusted in the connection profile itself to indicate that it does not need a client connection profile at all.
Command line options for OpenVPN Connect v3:
https://openvpn.net/vpn-server-resources/command-line-functionality-for-openvpn-connect/
Kind regards,
Johan