I think a third-party tool, such as iTextSharp, would be the best way to go in your situation. Using iTextSharp, you can in fact write to an existing PDF file. For example, have a look at this link and scoll down to "Examining step 4: adding content": http://itextsharp.sourceforge.net/tutorial/ch01.html
Also, since I'm guessing this file will periodically both be written to and read from, I'd pay extra attention to it's read/write attributes, locking, and things of that nature. All this I'm sure can be controlled with iTextSharp, and can be found in their documentation.
Oh, and lastly, I would also pay very close attention to the machine's CPU/Memory/resources while doing the write process. You never know how some third-party tool might handle it(that's not to say that tools/software on the market don't mess up of course). As a test, try writing a bunch of lines to the file inside a loop.