IMO, it is risky to import PDFs into iBooks. As you guys have seen, there is only one way to get them out, via email. It doesn't support the "Open In" dialog though you can transfer files into iBooks this way. Worse yet, if you do a backup, iBooks won't backup your PDF files, so if you backup and and restore, all of your PDFs will be gone. It might be worth trying to connect the iPad to a PC via the sync cable and seeing if you can copy them to your PC. Then move them back into to GoodReader. GoodReader will backup your stuff and when you restore, it will be there.