First of all, it is important to understand that PDFClerk Pro documents and PDF documents are not equivalent.
A PDFClerk Pro document has a proprietary file format that saves state information in addition to the PDF information of the PDF source material. It cannot be opened by other PDF editing software. You save documents in PDFClerk Pro format if there may be a need to work on a document over the course of multiple sessions. If no such need exists, all you may want to do is to print, or to export the result of a PDFClerk Pro document session to a new PDF document, without saving the PDFClerk Pro document itself. E.g. if all you do is to prepare a source PDF document for booklet printing, you may want to open it, impose it in 2-up layout and export the result to PDF. Then close the session without saving.