I am not sure this is the problem you are having, but often when you switch themes, or rename the theme folder, the menu assignment box get’s unchecked. If you go to Appearances -> Menu, select the menu that’s not working from the dropdown. After clicking on “Select” make sure that the checkbox under “Display Location” is checked. In the example below, I created a menu called Util Nav, and assigned it to a menu I registered in the theme’s function.php called “Utilities Nav”. If no checkboxes are checked then wordpress will use a default menu instead.
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