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If you want the sizes updated in Calibre, you must always use Calibre to change the format files. So, for EPUBs, run a Polish job on them to at least losslessy compress their images, and embed and subset their fonts.
I cannot think of anything for PDFs other than reconverting them to PDF or to EPUB. PDFs are problematic in the base case, so take care. Reconverting PDFs to PDF can change their layout so they do not resemble the original. PDFs are terrible ebook formats.
DaltonST
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