PDFPen and DTPro parsing

I use PDFPen to help me make notations in PDF’s that are stored in DT Pro. When I make a text notation in my PDF DT can’t parse that text item which means I cannot search for the note I made. However macos-x default pdf viewer can find the text. It appears that DTPro’s method for parsing the PDF is different from the way that apple parses the pdf. I can rectify the problem by printing the document and saving it as a pdf but that means I have to re-import it to DTPro which sort of defeats my purpose. Is there any way that this can be fixed? The ability to edit a pdf is important for me.

Appreciate any help in this manner. Perhaps automator can be uses - allthough I am very novis on using autmator