I cleared the thumbnail cache and reopened the folder in nautilus. The
previously missing file was now listed with the document icon and the
"loading" overlay (as though generating the thumbnail), but the
thumbnail never appears. After a minute or so, the loading overlay
disappears and I see only the generic document icon for the file. If I
close the window and reopen, I get the same behaviour as before.. the
file doesn't even appear at all in nautilus.

The 1 thumbnail now in my cache is for the missing pdf, and it looks okay in 
eog.
output from gconftool-2: evince-thumbnailer -s %s %u %o

-- 
nautilus doesn't show all files
https://bugs.launchpad.net/bugs/387319
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