Hey,
I used DTPO for the last four month and I am quite happy about the functionality 
I have different databases with focus on an academic workflow for my PhD-Thesis. Yesterday, I wanted to replace a document in my DTPO because I added comments to the PDF on a different mac. However, the original file were already linked to other documents.
My question: is there a way to replace a PDF without destroying the links of the original file?
Thanks for your help!
Nico
It depends on the kind of link.
If you have made a link back to the PDF file in an RTF file by option-command-dragging the PDF to the body of the RTF, then you can right click that link in the RTF file, select Edit Link from the contextual menu and replace the “x-devonthink-item” reference to the old file with the reference to the new file. (When you right click any document in DEVONthink you can choose Copy Item Link and put the proper reference link on the clipboard.)
If you have made an automatic wiki-style link by typing the name of the PDF into a document, then it’s a little trickier. You could open the old PDF in one window, and the new PDF in another. Display the sidebars so you can see the PDF pages. Carefully drag the annotated pages from the new PDF into the sidebar of the old PDF. Delete the pages you no longer want. And be sure to SAVE the file. You are saving the old PDF, which has had a page transplant. Do NOT rename the old file else all the wiki links will die instantly.