This was fixed thanks to @gouravshenoy. Since the zip from S3 was being extracted into the home of ec2-user, CodeDeploy was cleaning the entire folder (which happened to be where all other microservices were deployed). So the fix was to extract the zips into their own folders.
This was fixed thanks to @gouravshenoy. Since the zip from S3 was being extracted into the home of ec2-user, CodeDeploy was cleaning the entire folder (which happened to be where all other microservices were deployed). So the fix was to extract the zips into their own folders.