I spent forever editing the titles and authors of more than a hundred PDFs in iBooks, using iBooks list view on my computer. When I synced my iOS devices via iTunes, only a few of my files would show their new names on my iOS devices after syncing. I had to use different methods for different files to get them to show the edited titles and authors on my iOS devices. Some would show their new titles after syncing after I deleted them from iBooks, then dragged them from Trash into the desktop, editing the titles on my desktop, and adding them from there to my iBooks library. Other PDFs had to be altered by opening them from the desktop in Preview, exporting them as TIFF files, opening them again and then exporting them as PDFs upon editing title and author before adding them back into my iBooks library. Other PDFs just would sync the changes no matter what I did.
In the end I deleted all my PDFs from my iOS devices using iTunes, restarted all the devices and my computer, and them added the PDFs back to my devices using iTunes. I now have a completely well organized library of PDFs on my devices, but getting there was arduous, tedious and time consuming with countless syncs and restarts.
I can't say this for sure, but I got a feeling that whichever software used to produce the original PDFs was the factor deciding how easy or hard it was to get my iOS devices to take to my edited data. PDFs made with either Preview (from another file format) or PDFs made with any Microsoft Office program for Mac seemed to show my edited data without any problem. PDFs originally made with Adobe software or other software seemed to demand some work before letting my iOS devices show the new edited data. This is just a hunch, though. The PDFs that were the toughest to get to show new edited data, finally caved in by me using the PDF to TIFF to PDF before adding them back to iBooks.
It took a lot of effort, but now I finally have a library that's usable. I wish you the best of luck in getting there too.