Hi,
I have deployed Hybrid Calendar Service for both on-premise Exchange and Office365 for different instances but so far I have never come across a scenario like you mentioned.
In Webex Control Hub, you can integrate Hybrid Calendar Services with both on-premise Exchange and Office365 at the same time. If a user is present in either on-premise Exchange or Office365 then the calendar services should work. I have never tested it but I do not see any reason for not working.
Or as you mentioned, you can wait until you move to Office365.
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Thanks, Vaijanath S.