Restore ibooks library mac

I have had to put a new hard drive in my macbook so I restored it to my latest Time Machine backup. I also have a clone of the old hard drive on another external disk. I have had soooooooo many problems with this Time Machine restore, I am definitely changing my backup software from now on. Anyway, my iBooks Mac library didn't get transferred. I went into my old cloned drive and copied over the whole /Users/name/Library/Containers/BKAgentService to my new drive but iBooks still cant see that I have books there. When I open the application I get this:
I cant just redownload the books from itunes because they arent from there originally. Even if I go into the blank iBooks library and try to add all of my books to that, they just don't get added...
Preferrably I want to have a symlink to the ebook files and keep them on a separate drive. I tried doing this as well as having all of the files on the actual internal drive but neither way worked.
Any suggestions on how I can restore my library? Im thinking there must be another file outside of this BKAgentService folder that manages the library but I dont know where it would be...

Problems such as yours are sometimes caused by files that should belong to you but are locked or have wrong permissions. This procedure will check for such files. It makes no changes and therefore is not, in itself, a solution.
First, empty the Trash, if possible.
Triple-click anywhere in the line below on this page to select it, then copy the selected text to the Clipboard by pressing the key combination command-C:
find ~ $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 \) 2>&- | wc -l | pbcopy
Launch the built-in Terminal 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 Terminal in the icon grid.
Paste into the Terminal window (command-V). The command may take a noticeable amount of time to run. Wait for a new line ending in a dollar sign ($) to appear.
The output of the command will be a number. It's automatically copied to the Clipboard. Please paste it into a reply.
The Terminal window doesn't show the output. Please don't copy anything from there.

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