Why does itune delete my pdf when syncing?

Hi,
I'm just got a ipad air 2, and I'm totally new to apple both software and hardware. One thing I don't understand is why does iTunes prompt to delete my existing pdf in my ipad which I download from my email when I sync up with itune where I had some other pdf?  (under the ibook)
from a logical point of view my understanding of the word "sync" is to ensure both side (ipad and itune library) had the same data or files when there is a different in data/file. (correct me if i'm wrong)
pls advice on how to do a sync which ensure both side of data is same why syncing. as I travel around I don't always keep my doc in the itune computer.
IPad air 2 ios 8.1.2
regards
Soong

Syncing is from a computer to a device, when you sync it takes what you've selected on the tab in iTunes and replaces what you've currently got in the app on your iPad with that selection.
You should be able to copy them over to your computer's iTunes library via File > Devices > Transfer Purchases (though they aren't iTunes purchases that should copy PDFs and/or epubs in the iBooks app on your iPad) - and if your computer is a Mac with Mavericks or Yosemite on it then do File > Move Books From iTunes in its iBooks app to move them over to it. They should then show on the iPad's Books tab for selecting / syncing / keeping on the iPad.

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