Usually one would only apply media queries sparsely, to make small adjustments based on screen size. They may not be needed at all, if not for specific breaking points.
Caching normally applies to live web pages, a double refresh or a
CTRL+F5 should serve the latest files on the visitor’s end. Doesn’t look like you’re using a CMS or anything (that could also be caching server side) so that ought to work.