Deleting a ScreenSteps site that is connected to a Zendesk Help Center will not affect the Zendesk Help Center in any way. Only the content in ScreenSteps is affected.

Links between the articles in ScreenSteps and the articles in Zendesk will be removed. The result is that updating the articles in ScreenSteps will no longer update the articles in Zendesk.

For more information on what happens to articles in a site when it is deleted refer to How to Delete a Site.