Was trying to transfer my PDFs from my iPad to my new MacBook but they all disappeared... How do I get them back?

I just got a replacement MacBook, and only transferred my Documents, Music, Pictures, and Movies folders... Apparently my iBooks content is not stored in the iTunes folder so I just plugged in my iPad to transfer my PDFs into iBooks on my Mac and now they have all vanished from my iPad!!! How do I get them back?