Thanks for the replies everyone. At the moment I feel Zorin isnt working for me, lots of little annoying niggles, so I am probably going to go back to Mint.
The metadata is stored in the Calibre library directory, where Calibre copies added books. If you save that, you save everything related to the books themselves, and would only lose some application settings.
Ive set it up so that the Calibre library directory is located on the external hard drive - so hopefully then everything will have been saved, fingers crossed 
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