Please help me! iBooks delete all pdfs then uploads all at every sync.

Hi everyone, I need some help, much appreciated if anyone can give me a hand. I have hundreds of heavy PDF files I use in a daily basis for Uni, about 10GB in my iPad 3 (the one pre-air) is of PDFs. I ran into an issue today for the first time ever, I uploaded a new file to iBooks via ibook in the iMac (with Maverick) + iTunes as usual and the author had lots of unusual characters something like "%674f88uh7(*&" ok...after that file was upoloaded, all other pdfs started to freeze and not loading anymore. So I delete that file and after that nothing worked since. all files showing that loading icon but nothing..so I deleted my entire library (Noooooo) and uplaoded everything again. Now everytime I add a new pdf, the entire library (10GB) of books go grey, then disappear and start loading 1 by 1 all over again, no more incremental uploads like I used to have before/ I tried all settings possible, but again, if I hit sync on iTunes, the iPad library empties out, and starts loading all books, this takes a long hour to complete...I need help please, what am i doing wrong?
Thanks!

Ok, this has happened to me twice now. I've been using weave since pre-1.0.
The first time I needed to wipe a cluttered firefox profile, then re-merged my sync and while it restored all of my bookmarks, it only caught half my passwords.
The second time, today, I needed to reinstall windows. I connected to firefox sync and selected merge, but the only bookmarks merged in were those I added recently, likely since the 1.4 update.
This is very troubling to me as there was never any warning that all of my data would not be secure. It was my fault for depending on it but now several years worth of bookmarks are just gone.
Am I using it wrong? When a new version comes out do I need to somehow re-sync everything? One would think that is taken care of automatically.
Please let us know if there is a way to recover our lost data.
And for the sake of other users please track this down and consider warning people they could lose their data.
Thank you.

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Please help me! iBooks delete all pdfs then uploads all at every sync.

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