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Ah, I found a way to fix this. I opened up the epub in 7zip, sorted by size and deleted all the 100 byte images. Then opened it in Calibre's book editor and hit the "Check Book" option (which i'm guessing found all the lines of code referring to images that don't exist anymore and removing them).
Albeit if anyone knows a better solution, like finding and fixing the issue during conversion, would really appreciate it if you'd let me know!
Thanks!
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