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I've had issues with pdf draining battery as well. Sometimes rendering the PDF is cpu expensive. But if you're scrolling around a lot, that might also cause it, as screen updates eat power.
Sometimes converting or optimizing the pdf will reduce cpu drain. It's easiest on a mac, but you can use gs to do it in linux as well. The converter in calibre breaks formatting which occasionally is an improvement, but wouldn't be my first choice.
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