Calibre does not reflow PDFs as far as I know, though if it were a text based PDF you could convert it to a reflowable format using calibre, though PDF conversion is seldom ideal.
But these are scanned books? I.e., the PDFs consist of images, not normal text? Nothing can reflow that. Try running them through OCR software and see what the results are like. The OCR software will likely output reflowable format, like HTML or DOC, which you can convert (with calibre, or with calibre along with a word processor) to a reflowable ebook format.
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