Adding books from iTunes to Calibre

[hhharkness]

I used to have all of my eBooks both in Calibre ad iTunes, so I could access them on both my computer and my iPhone, but then I went and broke my old laptop (tripping over a cat, how else?) and as per my usual luck, my backup wasn't up to date.
Fortunately (or so I thought), the four books I didn't have backed up were still on my iPhone, so I extracted them to my new laptop using iExplorer. I was able to add them to my new iTunes library, however, when I look in the file location I can't seem to find the eBook files (which should be ePub).

When I connect Calibre to iTunes, select the books and click "Add to library", I get this;

calibre, version 1.11.0
ERROR: Add to library: Cannot copy books directly from iDevice. Drag from iTunes Library to desktop, then add to calibre's Library window.

However, when I try doing that, I get this message;

calibre, version 1.11.0
WARNING: Failed to read metadata: Failed to read metadata from the following:

The Lost Symbol.epub
Traceback (most recent call last):
File "site-packages\calibre\gui2\add.py", line 136, in start
File "site-packages\calibre\gui2\add.py", line 229, in add
File "site-packages\calibre\gui2\add.py", line 241, in add_formats
IOError: [Errno 13] Permission denied: u'C:/Users/Jonna/Desktop/The Lost Symbol.epub'


Angels & Demons.epub
Traceback (most recent call last):
File "site-packages\calibre\gui2\add.py", line 136, in start
File "site-packages\calibre\gui2\add.py", line 229, in add
File "site-packages\calibre\gui2\add.py", line 241, in add_formats
IOError: [Errno 13] Permission denied: u'C:/Users/Jonna/Desktop/Angels & Demons.epub'


The Da Vinci Code.epub
Traceback (most recent call last):
File "site-packages\calibre\gui2\add.py", line 136, in start
File "site-packages\calibre\gui2\add.py", line 229, in add
File "site-packages\calibre\gui2\add.py", line 241, in add_formats
IOError: [Errno 13] Permission denied: u'C:/Users/Jonna/Desktop/The Da Vinci Code.epub'


Inferno.epub
Traceback (most recent call last):
File "site-packages\calibre\gui2\add.py", line 136, in start
File "site-packages\calibre\gui2\add.py", line 229, in add
File "site-packages\calibre\gui2\add.py", line 241, in add_formats
IOError: [Errno 13] Permission denied: u'C:/Users/Jonna/Desktop/Inferno.epub'

And Calibre adds what seems to be 'empty' books to the library, which, when I attempt to open them, give me this;

calibre, version 1.11.0
ERROR: Cannot view: C:/Users/Jonna/Desktop/Angels & Demons has no available formats.

For each book.

[GRiker]

Unfortunately, Apple have made many changes to iBooks and iTunes recently that have broken calibre's interface (more details here).

G