As to why it happened, possibly you have the Sync function activated. Or perhaps the Sony Reader Library is redownloading the books from the Sony Store. I had that happen a long time ago. I wound up having to delete the application completely and reinstalling it. But hopefully it is just a Sync activated issue.

Probably best to turn OFF the sync function. I've heard a lot of bad issues using Sync and no good reports from using it. You can easily manage the books on your reader(s) without Sync. Just drag and drop whatever book(s) you want to the reader and then into the Collection(s) in which you want them. Right-click on a book to delete it either from a collection or from the entire reader.