ipad question-books

So on my ipad under the settings synching books is unchecked. if I check it then it will want to erase everything on my ipad. I guess this is because its synched with another library? The problem is it was synched with this computer but i did a format and reinstalled the OS so I guess its still looking for the old library? I have a backup wtih time machine can i resore the library so my ipad will see the old library ?

The other thing is I want to synch things manually so I guess thats the setting i want anyway? I guess it doesn't matter about the other libaray then?

My other problem is I have a large number of PDF on my ipad but not on my computer , I'm not sure where the orginial files are, is there anyway to transfer the pdfs back to my computer? I though there would be a way to email?

any advice would be apprechiated

if there is any clarifcation needed please let me know.