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No, there's no way to modify the PDF on the iliad. The scribbles are held in a separate file, so even writing on a PDF is not really writing *on* a PDF (if you see what I mean).
One approach you could take is to pre-process the PDFs and place them in a larger page size so that you have large margins at the side or bottom or to add additional blank pages at the end and jump to those when you need extra space (you could even add hyperlinks).
Doing something like this (on your PC, not the iliad) would require additional software (which you can get for free, even for windows). One way to do this would be to use latex (MikTex for windows). If you want to go down this route I could help out with how to automate what you want to do using latex.
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