This information is no longer valid as features have been added to the O365 product to allow you to manage your workflows. This article will remain in place but will be considered legacy.
If you've been wondering how to delete a workflow from our O365 product you will find when you remove it from the "workflow settings" menu it remains in the "open" dialogue in our workflow designer. Currently there is no way to remove that from the "open" dialogue within the product.
This will cancel ALL instances of this workflow running, orphan any tasks and any workflow history associated with instances of this workflow. Please use this at your own risk as once deleted the workflow CANNOT be recovered by Nintex. This is currently a work around for removing a workflow you no longer want listed in your "open" dialogue or want available to users in your site. Please use this at your discretion as it can have severe consequences if done to a workflow currently in use.
Here is my workflow that I deleted from "workflow settings" that is now stuck in the "open" dialogue window:
However leveraging SharePoint designer you are able to manually remove the workflow from your site completely. To start you will need Sharepoint Designer 2013. You can find the download link for SharePoint Designer here: http://www.microsoft.com/en-us/download/details.aspx?id=35491
Once you have downloaded and opened SharePoint Designer, navigate to the site in question your workflow is published at. Like Nintex Workflow for on-premise, we store our workflows at the site level. Once there, navigate to "workflows" under "site objects" and you will see a list of all workflows published on the site. Your workflow should be listed in workflows site object.
From there, simply delete the workflow and you will no longer find it no longer published in "workflow settings" nor will you see it in the "open" dialogue in Nintex workflow designer.