The DuplicateFileDocument action is used to, as the name states, to duplicate Filedocuments (to create a copy).
Perhaps you could gives us more context on what you are trying to achieve.
Is the PDF you already have created from data within your application?
Did you upload the PDF and do you want to add another PDF to the uploaded PDF (as in merge them) to create a new PDF existing of the 2 PDF's?
Do you have a master copy of a file document and want to duplicate that? More context would help.
If you are using the java action in a microflow then you would have to retrieve the master copy of the file document, create a new object (make sure the entity has a generalization of system file document), and then run the java action. In the java action there are parameters along the lines of source document and target document (not sure what the actual fields are called).