string strInputFile = @"F:\DEV\TEST\Input.pdf";
string strOutputFile = @"F:\DEV\TEST\Output.pdf";
// Open the output document
PdfDocument outputDocument = new PdfDocument();
PdfDocument inputDocument = PdfReader.Open(strInputFile, PdfDocumentOpenMode.Import);
// Iterate pages
int count = inputDocument.PageCount;

for (int idx = 0; idx < count; idx++)
{
   // Get the page from the external document...
   PdfPage page = inputDocument.Pages[idx];

   for (int a = 0; a < page.Annotations.Count; a++)
   {
      PdfAnnotation annotation = page.Annotations[a];
      annotation.Contents = "NewValue";
   }
   // ...and add it to the output document.
   outputDocument.AddPage(page);
}

// Save the document...
outputDocument.Save(strOutputFile);