No, you can only upload one PDF, sorry.
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How can I get a PDF version of a Leanpub ebook on my Kindle?
How do I switch to the Upload writing mode?
Is it possible to import chapters created as individual PDFs?
When uploading PDFs for a new book in the Upload writing mode, do I need to combine all chapters into one PDF, or can I upload a PDF for each chapter individually, which will be combined once published on Leanpub?