@Louis, in the past we’ve used the nav_menu_css_class filter, we’ve tested this with Cwicly/FSE and it doesn’t work due to nav_menu_css_class relying on the “old” way of displaying nav menus.
We quickly refactored our code to use wp_get_nav_menu_items and tested but it doesn’t seem to show classes added using this method.
I had a quick look at the Cwicly codebase and can see the reason, based on how the classes for nav items are created.
Please can you append the classes from wp_get_nav_menu_items to the menu items, or provide an alternative way of filtering the classes, then I will be able to share our general solution to this.
Thanks!