Elastic Beanstalk application failing to deploy - existing application seemingly broken - amazon-web-services

Question

We've been using EB for about a year, our main backend guy is not working with us at the moment. I've been deploying without any issues for the last 2 months, and today when I've tried to deploy I'm seeing this:
INFO: Environment update is starting. INFO: Deploying new version to
instance(s). ERROR: [Instance: i-dc773612,i-4073a981] Command failed
on instance. Return code: 1 Output:
[CMD-AppDeploy/AppDeployStage0/InfraWriteApp2] command failed with
error code 1: Error occurred during build: Command 01downloadVersion
failed. INFO: Command execution completed on all instances. Summary:
[Successful: 0, Failed: 2]. ERROR: [Instance: i-dc773612] Command
failed on instance. Return code: 1 Output:
[CMD-AppDeploy/AppDeployStage1/AppDeployEnactHook/01_flip.sh] command
failed with error code 1:
/opt/elasticbeanstalk/hooks/appdeploy/enact/01_flip.sh
++ /opt/elasticbeanstalk/bin/get-config container -k app_staging_dir
+ EB_APP_STAGING_DIR=/var/app/ondeck
++ /opt/elasticbeanstalk/bin/get-config container -k app_deploy_dir
+ EB_APP_DEPLOY_DIR=/var/app/current
+ '[' -d /var/app/current ']'
+ mv /var/app/current /var/app/current.old
+ mv /var/app/ondeck /var/app/current mv: cannot stat ‘/var/app/ondeck’: No such file or directory. INFO: Command execution
completed on 1 of 2 instances in environment. ERROR: [Instance:
i-4073a981] Command failed on instance. Return code: 1 Output:
[CMD-AppDeploy/AppDeployStage1/AppDeployEnactHook/01_flip.sh] command
failed with error code 1:
/opt/elasticbeanstalk/hooks/appdeploy/enact/01_flip.sh
++ /opt/elasticbeanstalk/bin/get-config container -k app_staging_dir
+ EB_APP_STAGING_DIR=/var/app/ondeck
++ /opt/elasticbeanstalk/bin/get-config container -k app_deploy_dir
+ EB_APP_DEPLOY_DIR=/var/app/current
+ '[' -d /var/app/current ']'
+ mv /var/app/current /var/app/current.old
+ mv /var/app/ondeck /var/app/current mv: cannot stat ‘/var/app/ondeck’: No such file or directory. INFO: Command execution
completed on 2 of 2 instances in environment. INFO: Command execution
completed on all instances. Summary: [Successful: 0, Failed: 2]. INFO:
New application version was deployed to running EC2 instances. ERROR:
Update environment operation is complete, but with errors. For more
information, see troubleshooting documentation. ERROR: Update
environment operation is complete, but with errors. For more
information, see troubleshooting documentation.
I have no idea why, as far as I can tell I've committed/deployed everything as I normally would.
I see the latest commit when I go into 'Application Versions' - and it would appear that is is deployed (it has the environment name next to the commit in the Deployed To column). However my mobile applications are no longer able to connect to the PHP files on the server, they keep getting 403 forbidden - even on files which were not changed in the last commit. It's as if the application is not there since the deploy failed.
Where should I go from here?
Edit: I've investigated a bit further, and the upload seemed to be successful as I can see the zip file is there. It's the deploy part itself which is failing. I've tried rebooting instances, as well as stopping instances and letting the load balancer create new ones. Still everything fails, although now I get a timeout. From start->timeout is taking less time that the timeout limit of 30 mins, the timeout happens in 5-10 mins.