The problem is related to the “Advanced custom fields Pro” plugin included into your theme. It’s marked as compatible with WordPress 5.2. But WordPress 5.4 includes long waited related update – it calls itself the ‘wp_nav_menu_item_custom_fields’ action, which allows to add custom UI elements to the front-end menu administration page. Outdated version of “Advanced custom fields Pro” calls ‘wp_nav_menu_item_custom_fields’ itself. That was a reason of duplicate output from URE Pro. I added checking if output for menu item was done to exclude similar issues in future.
I uploaded the updated version of code to your site. Thanks for your help with investigating this problem.