No. All photos must be included in every sync - each time that you sync. If you copy the photos from the one library into the other library - and then select the new photos along with the current photos to sync - then they will all sync to the iPad.
if you simply choose the new library to sync, it will replace the photos currently on the iPad.
Thanks for the answer. Since my photo library is so large, I broke it up into two libraries. Now I am thinking of opening a third library. Not all of the albums are worthy of including on the iPad, so I will create a library of only the ones I want to include on the iPad. Your answer was what I needed.