I wasn't able to reproduce this issue. Here were my steps in the
terminal:

rm -r .cache/thumbnails/
wget 
https://upload.wikimedia.org/wikipedia/commons/d/dd/CA_Whittier_301366_1965_24000_geo_%28PDF%29.pdf
nautilus

After the window opens, I can see the thumbnail of the pdf I downloaded with 
wget successfully.
I also downloaded evince with apt and selected it in the "Open with..." picker, 
toggling the "Always use for this file type", and repeated the steps

rm -r .cache/thumbnails/
nautilus

and it still loaded successfully. Can you share any steps you did so I
can try to reproduce the issue?

I also saw in the KernLog.txt that there are apparmor denials for
/usr/bin/evince-thumbnailer. Evince ships its own apparmor policy in its
own package. We can try adding the rules that addresses those denials in
the profile but I'd first like to understand how this happened.

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https://bugs.launchpad.net/bugs/2143235

Title:
  no pdf thumbnails

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