If you'd like, there is a feature in the ePier exporter that you can copy to the Google Base Feeder. It is a conditional statement near the beginning of the output section (after the products_query) that starts writing at 'X' number of products. So, you'd first put start = 1, max_products = 1000, then start = 1001, max_products = 2000 and so on.
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