This post does not needs replies but should serve as a solution to help combat this problem should it happen to someone else. I did not really find any documentation about this so this should serve as a initial guide.

ISSUE

When trying to publish a new solution on test to roll back the version back to production version it says an application has an ongoing publish. 

Solution <-- Provided by outsystems support.

IN CLOUD.... Contact outsystems since you can not perform step 1 :)

ON premise follow these guidelines.

• Please perform the following operation on the affected environment: Access the remote server, open the Windows app Services, search, and restart the OutSystems Deployment Controller service. After that, try to publish again.

You can also find more steps to try in case the above solution does not work:

• Rollback to a Previous Version
  Unable to deploy applications using LifeTime see link below https://success.outsystems.com/documentation/11/managing_the_applications_lifecycle/deploy_applications/rollback_to_a_previous_version/?

If this does not help contact support!

Once again thanks to Outsystems support!