Hello, Have a subscription to Interface Pro. For some reason our sub-menu’s have become corrupted and no longer work. You can see here: http://lenape8.org/
I have tried uninstalling plugins, changing menus, and multiple other fixes. The only thing left is to re-install the theme. If I re-install the theme by copying the files via FTP, will that overwrite any custom CSS and other changes I made through the custom menu?
If you have added css files in Custom CSS then no worry. Nothing will be lost and you are safe.
If you have code customization in theme for example javascript file, php file and css file then only that code will be changed.
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