Did you go into your AWS Console like I suggested? Because you should see that cert listed in the Certificate Manager section. It has a column for "in use". Is it in use?
More details are shown when you click on the cert in that section. One of those detailed categories is "Associated resources". What AWS service is listed, if any? Are you still using that service? Only you can know whether it is needed.
Mind, this really has nothing to do with Let's Encrypt. I happen to know this because I have an AWS account myself and use those services.
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