I used:
ls -lR | grep -v -e <string>
at the top level of the image upload folder, where string was either the owner or the permissions, to check that. I did not find any files with the wrong permissions or ownership.
refreshImageMetadata.php -f
does not say that it refreshed the files (~80 of them) in question. pdfinfo is able to run against all of the files in question sufficiently to report the PDF version. PDF versions for these files range from 1.3 to 1.7.
FILES=$(find $PREFIX -name "*.pdf" -type f | grep -v "/temp" | grep -v "/deleted" | grep -v "/archive" )
for F in $FILES; do
echo $(pdfinfo $F | grep "PDF version") $F
done
So, there are about 80 of these files with the 'red A' thumbnails. Apart from the likelihood of error, we could re-upload all of them to get the new thumbnails. We would prefer not to need to take that approach. Also, there is the concern that this symptom betides some problem that will bite us later.
Thanks again for your help.