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Hey
Its sounds like the CloudFormation stack could be drifted. Is it possible the Security Group was deleted? It does not have to be via the UI but if its done outside the Beanstalk service (e.g. CLI delete-security-group) then we could expect to see this error.
Resolving some of the behaviour by changing the launch template via the EC2 UI should really not be required. Everything should be done within the scope of Beanstalk i.e the Beanstalk Configuration page in the UI, the eb cli or the API.
I would suggest cloning [1] the existing environment and confirming it has the same errors. Then rebuild the new environment [2] so that it will "restore it to a working state. Rebuilding an environment terminates all of its resources and replaces them with new resources with the same configuration." IF you confirm the new environment is working as expected you can then swap the CNAME URL records [3]
If this does not resolve the behaviour I would look to create a new environment with the desired platform and configuration. Deploy your application and swap the CNAME records.
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Thank you for the help. I updated my question with the status of the website (tldr; it's fine, operating as expected, not down). Would your suggestion on how to fix this still be relevant if the website was operating as expected and the only issue is localized to the Elastic Beanstalk page?