How do I flatten a PDF so that the elements I've added in PDFpen are no longer editable?

There are several ways to flatten a document. Using the latest version of PDFpen/Pro, you can export to a flattened PDF via File Export. 

Otherwise, additional options are to:

a. Saving via Print (File > PRINT > PDF > Save as PDF) to flatten the document annotations
b. Saving via PDFpen as a .TIFF file (depending on your PDF, this can save your page(s) as one large image)
c. Encrypting the document via Owners Permission (PDFpenPro only) to restrict editing.
d. Scanning the document

Note that using the Print to flatten method, annotations should all flatten, but bitmap images may not (meaning, if you open the document in another PDF editor, you may still be able to select the bitmap image).