You could try one of many open-source (and therefore free) options (here might be a good place to start looking). This page says that:
You cannot make permanent changes to PDF files using Adobe Reader; however you can perform many edit-like functions using Adobe Reader if the author has enabled these functions using Acrobat 7.0 Professional. For example, you can highlight text and add comments on sticky notes.
So it would seem that you may be able to what you are asking about, though exactly what constitutes a "permanent change" is not mentioned.
I personally would try OpenOffice, as I have had a very nice time with it in the past and it is likely have the ability to import and export documents.