All images are laying in the root folder of dokuwiki. So you can do
$> cp -f favicon.ico lib/tpl/dokuwiki/images/favicon.ico $> cp -f logo.png lib/tpl/dokuwiki/images/logo.png $> cp -f apple_icon.png lib/tpl/dokuwiki/images/apple-touch-icon.png $> touch conf/local.php $> rm -rf data/cache/*
from within the root.
The $> touch conf/local.php resets the update hints (yellow boxes).
Or just use this bash script:
#!/bin/bash cp -f favicon.ico lib/tpl/dokuwiki/images/favicon.ico cp -f logo.png lib/tpl/dokuwiki/images/logo.png cp -f apple_icon.png lib/tpl/dokuwiki/images/apple-touch-icon.png rm -rf data/cache/* touch conf/local.php echo "Reset of icons and logos was successful!"