Thanks duckeedoug. It looks like the file I want is cache2.xml in the sync folder of the SD card. It seems to contain all the collection information. I've copied it over to the PC and hopefully this is all I will need to replace the next time my collections disappear.
My assumption is that this file is updated each time I make alterations to the books in the collections, and all I have to do is make a backup of it after every change.
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