PDFNet SDK supports exporting
annotations to a format called XFDF. XFDF annotations can then be
re-imported into the document with either the PDFNet SDK or third parties (line
Acrobat). The following blog post has more details:
We also provide sample code showing how to use XFDF. This sample is included with the SDK (http://www.pdftron.com/pdfnet/downloads.html), so you can run it and try out annotation export/import in your environment: http://www.pdftron.com/pdfnet/samplecode.html#FDF
Just to clarify, you do not have to save the PDF to use (or export) XFDF. You can add annotations to an in-memory
copy of the PDF, then export the annotations to an XFDF file without ever
saving the modified version of the PDF to disk. An in-memory copy of a
PDF is only written to disk when PDFDoc.Save() is called on it.
(The PDFNet SDK even supports creating a new PDF in memory, adding content and annotations to it, and exporting the annotations to an XFDF file, all without ever saving the PDF itself to disk.)
Similarly, when viewing the annotated PDF, you aren't required to first save the annotated copy to disk.