It appears as though the site will only use a new twig file when in development mode, but not in normal production mode.
This is 8.6.3 multi-site set up.
Things I have tried:
When caching is enabled, this is the last twig file that gets loaded:
<!-- BEGIN OUTPUT from 'themes/themename/templates/region/region.html.twig' -->
When caching is disabled, all the other twig files are loaded as expected.