Can't deploy to AWS Elastic Beanstalk after timeout

I am newish to AWS Elastic Beanstalk and this is the first time I have encountered this issue. I tried deploying a new version via zip upload of my app to an instance and the updated completed with errors:

"Completed but with Command Line Timeouts", I increased the timeout in the config file and redeployed, after which I got this message.

During an aborted deployment, some instances may have deployed the new application version. To ensure all instances are running the same version, re-deploy the appropriate application version.

This repeats each time try to redeploy.

I went into the EC2 instance and noticed the the /var/app/ondeck folder was still there.

I assume this is the issue, but i doubt that simply removing this directory would be the answer - unless it is that simple.

The /var app/current version is still present and the app runs fine using the version that was deployed prior to the initial timeout.

I inherited this app it is Laravel and the composer scripts take a while to run.

Thanks for any help.