Get rid of the DRM first. They'd be useless without an amazon account otherwise.

I do this, but not with rsync. I put PDFs and books that I want to read into my Dropbox during the day. When I get home I bidirectionally sync to my kindle dx with Unison (http://www.cis.upenn.edu/~bcpierce/unison/). I wouldn't trust my books with Amazon, ever.