You should be able to copy the PDFs to your computer's iTunes via File > Transfer Purchases.
Is there an account logged into the iPad (Settings > Store), and are there any apps from the iTunes store on it ? If there are apps then they will be tied to the account that bought/downloaded them, so unless that account is authorised on your computer's iTunes then they will be removed if you sync to your computer. If there is an account logged in on it then you can tap on it and log out of it and then log in with your account.
Anything that it is on your iPhone won't be affected.