The best option to transfer annotations from one document to another is via XFDF (or via pdftron.FDF.FDFDoc) . As a starting point please take a look at FDF sample project:
http://www.pdftron.com/pdfnet/samplecode.html#FDF
It shows how to do annotation roundtrip. Btw. technically you don’t need to export annotations to an external file. You can use the following line:
pdf_target.FDFMerge(pdf_source.FDFExtract(PDFDoc.ExtractFlag.e_annots_only));