Does anyone have insight into how renewing CAC's work with IPPS-A implementation?

"IPPS-A does not communicate with any Army legacy system" is untrue*. I'm not sure why someone at the RAPIDS office would tell you that unless they had not completed any of the training available regarding IPPS-A.

Did your unit actually update your record in IPPS-A (not iPERMS)? If your unit does not know how to update your contract extension, suggest to your PAC that they watch the training video on how to do Contract Extensions.*

Lastly, if your unit has accomplished everything they should be doing (uploaded the extension through IPPS-A), then have them submit a CRM on the issue or contact the IPPS-A Help Desk*
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* IPPS-A Interface chart - https://ipps-a.army.mil/Release-3/Systems-Impacted/
* Contract Extensions - https://www.youtube.com/watch?v=9SUpSNG-Pww
* IPPS-A Customer Support - https://ipps-a.army.mil/Contact/Customer-Support/

Your contract information must be manually updated in IPPSA to reflect your extention and new ETS date. It should be a retention responsibility, but most don't have access or knowledge of how to do so. Some S1/HR PROs have access and can do it, but also may not know how.

I believe this is a unit issue. I can't tell you how S1s have struggled with this. I would just your STP to see if your ETS has changed before you go back to the ID card Office.