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I agree--load smaller batches at a time. That way, if there is a book that is causing problems you'll be able to narrow in on which book is causing the problem.
I don't think having a 1000 books should be a problem--depending on the types of books they are. For normal AZW files that should be fine. I have 1,133 on my Voyage and don't have any problems with it slowing down or freezing. I did however load those books in smaller batches and as Harry suggested waited for the Voyage to complete it's indexing procedure with each batch before loading the next batch.
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