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There is (in my experience) just ONE way:
Completely convert (with apropriate software) the PDF in another format. You describe a common PDF-issue which is more or less irrelevant when staying in 'normal'-mode with unaltered formatting.
PDF never was intended to use in a way which reformates a file completely. There are lots of ways to let a PDF looks like it looks (reaching from just beeing a picture to reflowable text).
For a PDF looking the way you describe I do following:
1) Crop the pages to remove headers and footers
2) Load it into the ABBY-PDF-Transformer (comm. software)
3) Convert it to HTML-file
4) load it in WORD and convert it into RTF (this step corrects some issues with picture-sizes)
5) Load it a second time in Word
6) Save it back to HTML
7) Import in Calibre
8) Convert it into EPUB
9) Copy it onto the reader
I tested a lot of solutions described here and on other places on the internet and ended up with this 'simple' procedure. This corrects your problem and does a very good job to get a PDF with pictures in a useable EPUB-document. But I do not recomment it for it is not a quick solution.
A.
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