I would double-check by examining the filesize of the PDF stored in calibre, and/or opening it in the same software used to read the PDF pre-import.
Also, disable reading PDF in the builtin viewer. See Preferences ==> Behavior ==> Use builtin viewer for ...
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calibre does not modify ebooks during the import process, thy should be byte-identical. Thirdarty plugins of the "filetype plugin" type can, however.