How can I delete failed .ebextensions script?

I have Elastic Beanstalk environment and .ebextensions directory in root of my project. .ebextensions contains few scripts which run successfully. I added new script with 'commands' section in it. It contains one command to be executed in ec2 shell. The issue is that this command does not return SUCCESS result so it stops EB deployment from succeeding. I tried to fix it by deleting this script from .ebextensions directory and deploy new version without it but in logs I can see that EB still executes it and it stops EB deployment from succeeding. How can I delete this script so EB will not execute it ? Is it stored directly on ec2 ?