I'm not sure what they right answer is if you are doing in bulk as you will be creating duplicates as you mentioned. i'm assuming you are not using Directory Connector or the Azure App or some other SCIM. If users are in the system manually you could have every user log in and change their own email address and they will keep their settings. If you are using the Directory Connector or Azure i would think it would be as simple as changing the attribute, say from UPN to Mail, keeping the accounts as is; if that is what is going on.
Additionally, there might be an API you could use. Getting started with Webex | Webex for Developers
You can test all of these scenarios in the Webex Enablement Lab in Cisco dCloud.
