I managed to get hold of a friends Macbook and could backup all my files
off of it. I don't know why it wasn't working on my own PC. I'll just use
his in the future.
Thanks for your assistance
Hi garths11135488,
Thank you for letting us know about what you found.
I also investigated the problem (of failing to back up folders containing files and subfolders) with Apple's iTunes (desktop app).
I used iTunes for Windows 15.2.4 on Windows 10 and iTunes for Mac 15.2.4 on macOS Sierra (10.12.2). iTunes 15.2.4 is the latest version as of this writing (January 14, 2017).
Here are my findings.
Apple's iTunes for Windows has a defect where drag & dropping folders from the Adobe Acrobat Documents area in iTunes to any location (including Desktop) on a Windows computer does not copy the folders. It fails silently and does not show an error dialog. (I tried with an administrator account and "Standard user" account on Windows 10 and got the same result.)
Drag & dropping files still works with iTunes for Windows.
This is a defect in iTunes for Windows only. iTunes for Mac does not have any problems with backing up folders by drag & drop.
A workaround for the iTunes for Windows problem is to select files and folders in the Adobe Acrobat Documents area and click the Save to... button (instead of drag & drop).
Since iTunes is an Apple product (not an Adobe product), we are unable to fix the defect at our end. However, you can report the problem to Apple directly.
iTunes for Windows - Official Apple Support Communities
Feedback - iTunes - Apple
I also added a note to the FAQ document so that other Windows users will be warned.
How to back up and restore PDF documents on iPad/iPhone using iTunes
Thank you very much for sharing your backup experience!