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Hi, I guess that you use such templates: https://aws-quickstart.github.io/quickstart-atlassian-jira/ In that case, updating the Atlassian applications boils down to using a new AMI that they release. So, if you started your Atlassian app, it boils down to changing the AMI id in the template.
How it works is described here: https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/updating.stacks.walkthrough.html#update.walkthrough.ami
