Under settings (main iOS settings not within the app), how many books do you have it set to keep, mine is set for the latest 5 and used to do this every so often
I dont use the iOS very much now due to this issue, I have a 64 GB iPod and the app cannot store all my books successfully (less than 100)
it seems that iOS apps have access to a very small amount of storage, when this is reached the OS auto deletes things
closing apps makes a huge difference to how it works for me, double click the home button to see all suspended apps at the bottom, click and hold and then removing these
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