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I had the same problem with a NodeJS Elastic Beanstalk app. However, I was able to get around it by updating the Listener/Certificate settings via the AWS EC2 console (https://console.aws.amazon.com/ec2/), via the Load Balancers section (under LOAD BALANCING).
I was updating the certificate for a staging version of a cloned environment. This was the only way I could assign a different certificate to the staging environment.
See more at http://docs.aws.amazon.com/elasticloadbalancing/latest/classic/elb-create-https-ssl-load-balancer.html
Source:stackexchange.com