Follow-up to this issue.
Before another test upgrade I ran this in my files folder:
find . -name '*.*' -exec sh -c ' a=$(echo "$0" | sed -r "s/([^.]*)\$/\L\1/"); [ "$a" != "$0" ] && mv "$0" "$a" ' {} \;
With 45 journals / 50 gigs of files it did not take too long to convert all extensions to lower case.
I still had around 50 errors regarding files not being found, but it seems that these files are actually missing. Our installation is 10 years old, so I guess that is no wonder.