After updating from 7.1.0 to 7.3.1 the mobile menu icon and the mobile menu have disappeared at the 768px breakpoint. Also if you inspect the code in the browser the lines id="menu-line" and id="menu-button" have disappeared. On a similar site at v7.1.0, the mobile menu icon does show and the above code lines are there.
Should the CSS and JS folders and files be in the theme folder or the root directory, or does it matter? They are currently in the root and the header.php file points to them there, everything else seems to work OK.
The site with version 7.1.0 does have these files in the theme folder though and the mobile menu does show OK.