You will find the clear and exclude options on the metadata form of each object type (e.g. articles, galley, supp files) you have configured to assign the DOIs to. For example for articles, as editor you will find these options when you edit an article metadata form ( Editor > Submissions > articleID > Summary > Edit Metadata):
* Select this checkbox to clear the existing DOI for this article.
* Exclude this article from assigning it a DOI.
Also, on the issue data page you will have the options to clear and exclude all objects of that issue:
* Exclude Issue Objects
* Clear Issue Objects DOIs
Does this help?