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Hi,
Although it is not possible to associate a new AMI to a running instance, you don't have to worry about the running instance. When you deregister an AMI, it doesn't affect any instances that you've already launched from the AMI. The only thing is it can't be used to launch any new more instances.
Deregister your AMI - https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/deregister-ami.html
If the deleted AMI has custom configurations, I would also recommend you create a new AMI form the already running instance so that you can launch new instances with those custom configurations in future.
Thank you for the response. "If the deleted AMI has custom configurations, I would also recommend you create a new AMI form the already running instance so that you can launch new instances with those custom configurations in future." This means the running EC2 instance(EC2-A) may not have an associated AMI (AMI-A) but we can create a custom AMI (AMI-B) from that running instance and that custom AMI(B) can be used to create a new EC2 (EC2-B) when the need arises/EC2-A got destroyed. That's good to know. Am I correct?
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Yes, you are correct. You can find the instructions for creating an AMI from an existing instance in the EC2 User Guide at this link: https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/creating-an-ami-ebs.html