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Hi Adam,
You would need to remove the Blue/Green deployment before updating any extensions as this would be a DDL operation and would break replication. Once Postgis is updated, you should be able to recreate the deployment and attempt the update. Just make sure all of the databases have been updated too.
https://repost.aws/knowledge-center/rds-postgresql-upgrade-postgis https://docs.aws.amazon.com/AmazonRDS/latest/UserGuide/blue-green-deployments-overview.html