The cryptostream writes to a filestream. The XML can't write to the same stream, and if you use a different stream you'll either overwrite (this is probably your situation) or it'll append the XML after the encrypted information. The other option is the XML is written first, then appended or overwitten with the encrypted information, neith seems to apply in your case.
In your position I'd replace the file stream with a memory stream for the cryptography stuff. I'd perform the write immediately, reset the position to 0 and pass the memory stream into the Export method. Then all the XML writer has to do is to read the Memory stream into the file stream when you've reached the correct point in the file (or set a property to its contents).
The other problem you might face is that you need to encode the encrypted bytes (e.g. into Hex characters), otherwise you'll get non-printing characters in the XML document, fouling it up.