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You can upload a PDF to the system in the form of an image. You'll just need to host it on an online web album somewhere so that you can link to it. We don't however allow for direct links to be given within the query letters, so please refrain from doing this. (i.e. www.pdfofmybook...)To upload the image, you just need to press the little button of the sun and mountains (like the one you can see in the forums here!) and add in the link.
Alternatively, if you try to use a different browser such as Safari, this may help the formatting issue during the import from Word.
We suggest that you resubmit your work through AgentInbox and just update your query to reflect the newly edited version. Agents receive updated submissions relatively regularly, so sending in a query a second time around is not a disaster.
Hope that helps!
Hannah from the WEbook Team