How to transfer files from iBook to reader?
The first step is to export the PDF from iBooks to your computer (this cannot be one on your iPad or iPhone). Connect your iPad or iPhone to your syncing computer. Open iTunes. Select your device (how to do this depends on which version of iTunes you are running). Click on the Books tab at the top. In the current version of iTunes 11, I had to choose to view by PDFs. Then I could drag a PDF from the iTunes window to my Desktop.
Then follow the instructions in this document to import the PDF(s) into Adobe Reader:
Not so easy, I'm afraid. Easier if you just keep copies of your PDFs on your computer.