main navigation menu disappear after adding jquery source file

jQuery is already being included on the page, so you don’t need to include it again.

I’m assuming your adding that because you want to run the JS below it?

$(document).ready(function() {
    $("#countryChooser").change(function() {
        if ($(this).val() !== "") {
        var selector = "." + $(this).val();
        $('.box').not(selector).hide();
        $(selector).show();
        } else {
        $(".box").hide();
        }
    }).change();
});

If that’s the case, remove the additional call to load jQuery, then change all the $ to jQuery.

For example…

jQuery(document).ready(function() {
    jQuery("#countryChooser").change(function() {
        if (jQuery(this).val() !== "") {
        var selector = "." + jQuery(this).val();
        jQuery('.box').not(selector).hide();
        jQuery(selector).show();
        } else {
        jQuery(".box").hide();
        }
    }).change();
});