It’s as if pure-ftpd is ignoring its config files and secretly fetching a certificate from somewhere else.
I’d probably stop the service fully, and then start it again under strace to see where it’s reading that cert from.
/etc/ssl/private/pure-ftpd.pem should be a symlink to /etc/ssl/ssl.combined on a clean install however, and that should itself link to ‘/srv/example.com/config/ssl/current/ssl.combined’, which should be valid and up to date.