Clover Duo currently comes with the Mini for cardholder interaction (i.e. - cashier rings up the transaction on the Duo tablet, cardholder interacts with the mini to complete the transaction). My question is can the mini be swapped out and the flex be used instead? Without significant changes to our full integration certification?
No, you cannot just swap in a device type of your choosing.
Is it possible to do it programmatically through another certification? We have a some customers that would rather use the Flex to preserve counter space. Originally we were offering them the Clover Station Pro 2018 - which would've allowed the cashier to rotate the screen to let the cardholder complete the transaction.
If you have a question about certification, you should ask developer relations directly. I don't think a given app approval is tied to a specific piece of Clover hardware. I was answering your technical question about the Duo, you cannot use a Flex at the non-display end of a Duo technically.
We also noticed that the Clover Flex HUB came with the dev kit but did not come with production orders. I tested the hub on a production device and it was able to get power and wired network connection from it. I can only find the device on 3rd party sites, but the graphic that appears with it suggests connectivity to a Clover tablet, clover mini, and what looks like a 3rd party POS icon. See attached. 
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