Elastic beanstalk deployment failing few success and then failed it will happen on workers

Hello. 

You are facing an error while deploying your AWS Elastic Beanstalk (EB) environment. 

.032769 [ERROR] An error occurred during execution of command [app-deploy] - [FlipApplication]. Stop running the command. Error: remove current dir failed: unlinkat /var/app/current: directory not empty

As we can check from the error message, eb-engine tried to remove a directory '/var/app/current' but failed as the directory is not empty. 

To troubleshoot this, you need to access to your EC2 instances and empty the directory If there's any unnecessary files in it. 

I can't analyze this issue you shared only with the error message, so I would like to recommend you to open a support case via AWS Premium Support [1] and have professional assistance from support engineers. 

Regards, 

Myungsup Kwak  

Reference: 

[1] AWS Premium Support 

https://support.aws.amazon.com/#/contacts/aws-account-support