So, I am unable to retrieve my pdf's after the upgrade. Are they gone for good?
Unless you were forced to do a restore through iTunes on the computer, your PDF files should not have been deleted. But, because we got a new iBooks app, it's not impossible that something went wrong and the library was reset.
But the bottom line is, if your PDF files disappeared from iBooks on the iPad then the only way to recover them will be to download them again. Hopefully you have copies elsewhere or remember where you got them from.
Mild Ranting Below:
I've said this before, but it's worth repeating. Never rely on your iPad as the only place you keep important photos or documents. This is true of any device or even online services, but it goes double for portable devices. They are far more likely to be damaged than a computer.
Even backups are not 100% reliable. One, they don't include everything. Apple's media apps assume everything you put in them is from an iStore, and retrievable from there. Unless you add the content to iTunes on a computer first, and sync from there, you have no backup of those files.
You only have one backup, the most recent. This means that if you happen to do a backup after something is lost, then it is no longer in the backup to be restored.
Also, backups are all or nothing. You can't restore just one or two files, which means you risk losing recent work. It becomes a question of what is more important, those files or the work you've done since the last backup.