Why does iBooks (Mac) keep taking my PDFs off my iPad iBooks?

Question

I updated to OSX Maverick and I mostly happy BUT I have a MASSIVE collection of pdfs that were organized and layed out the way I wanted them in iBooks on my tablets. When I synched my tablets to update my backup, the books literaly vanished off my iPad.
I can't restore the libary for some reason, everything I do to add the backups on my mac desktop doesn't work. It's not as easy as 'drag and drop' prior to Maverick was. and the one method I get that lets me the ability to upload my folders of organized pdfs keeps getting them kicked back as 'You don't have access to the folder Temporary'.
It's the first big step BACKWARDS I've ever had with an Apple product and one that given the size of my pdf book library (over 600 organized/sorted books) is getting a bit annoying.

Answer 1

Launch the Console application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Console in the icon grid.
Step 1
Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left. If you don't see that menu, select
View ▹ Show Log List
from the menu bar.
Enter the name of the crashed application or process in the Filter text field. Select the messages from the time of the last crash, if any. Copy them to the Clipboard by pressing the key combination command-C. Paste into a reply to this message (command-V).
When posting a log extract, be selective. In most cases, a few dozen lines are more than enough.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Important: Some private information, such as your name, may appear in the log. Anonymize before posting.
Step 2
In the Console window, look under User Diagnostic Reports (not "Diagnostic and Usage Messages") for crash reports related to the crashed process. The report name starts with the name of the process, and ends with ".crash". Select the most recent report and post the entire contents — again, the text, not a screenshot. In the interest of privacy, I suggest that, before posting, you edit out the “Anonymous UUID,” a long string of letters, numbers, and dashes in the header of the report, if it’s present (it may not be.) Please don’t post other kinds of diagnostic report — they're very long and not helpful.