The first file creates a new model and pairs it with a controller

Facet.js

var Facets = Spine.Controller.sub({
    tag: "li",
    events: {
        "change": "click"
    },
    init: function(){
        this.item.bind( "update", this.proxy( this.render ));
    },
    render: function(){

        this.html( Mustache.to_html(searchFacetTmpl,this.item) );
        !this.item.count ? this.$el.addClass('empty') : this.$el.removeClass('empty');
    },
    click: function(){
        //This code works
        //Facet.find(this.item.cid).updateAttribute( 'checked', this.el.find('input').prop('checked') == 1 );
        //This code affects permanent changes on my model
        this.item.updateAttribute( 'checked', this.el.find('input').prop('checked') == 1 );

    }
});

setup.js

    var typeFacet = Facet.create({
        id: type.filter,
        filter: type.filter,
        title: type.title,
        checked: type.checked,
        count: type.count,
        type: 'type'
    });
    typeFacet.save();
    new Facets({
        item: typeFacet,
        el: $jsFilterPanel.find( ".js-" + typeFacet.id )
    });