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Default programs on linux are an utter and absolute mess. calibre uses Qt which in turn uses xdg-open. So you need to set your default PDF viewer in a way that will work with xdg-open. Open a terminal, run
xdg-open file.pdf
to test it. How you change the default for xdg-open is completely distro and desktop environment specific. Personally, I gave up on linux's default programs long ago and just wrote my open replacement for xdg-open.
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