I cannot link my PDF files on iPad to itunes

Gents,

I have reinstalled Windows on my desktop, and now I am trying to copy back the pdf files from my iPad 2 to iTunes.For some reason, itunes sees only 2 directories, "pfd" and "books" and ignores all other directories that I have created on the iPad. It also does not see any pdf files on the iPad that I created myself. This is rather irritating. I can read all the stuff on my iPad, but I would want to keep the copies in iTunes. What shall I do?

Sincerely,

Alex