In the management console, go to the Extensions section. Click on the extension in question, and one of the options on the top menu bar is Send Welcome Email (it's the option farthest to the right). That will send the provisioning file to the email address configured for the extension. You can also select multiple extensions and send several emails at once.
With 12.5 we also seem to have lost the ability to "manually" set up 3CXPhone: they don't seem to work right unless you set up your account using a provisioning file. Not sure exactly what's different.