My apologies for the inconvenience. The problem is WordPress uses ‘nav_menu’ taxonomy for menus.
This plugin uses global terms(only terms from the main site). So, any existing menu for sub site will need to be updated manually to make them visible.
To be honest, we do not suggest using global terms unless and until it is very important to share terms. It is not a great choice if you plan to move sub sites to independent sites in future. Also, I had a look at the current implementation and It will need some update for meta tables.
Hope that helps.
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