Duel logos for Pipeline (mobile/desktop) tested with v4.5.1 - Two files in this GIST - header.liquid and a new file nav-contents-2.liquid

header.liquid

{%- assign transparent_header = false -%}
{%- if template contains 'collection' and collection.image and section.settings.transparent_collection -%}
  {%- assign transparent_header = true -%}
{%- elsif template contains 'article' and article.image and section.settings.transparent_article -%}
  {%- assign transparent_header = true -%}
{%- elsif template contains 'blog' and section.settings.transparent_blog -%}
  {%- assign transparent_header = true -%}
{%- elsif template contains 'page' and section.settings.transparent_page -%}
  {%- assign transparent_header = true -%}
{%- elsif template == 'index' and section.settings.transparent_home -%}
    {%- assign transparent_header = true -%}
{%- endif -%}

<style>
  .header--transparent:not(.header--sticky):not(.header--stuck) .nav--desktop .main-menu>li>a{
    color: {{ section.settings.transparent_text_color }};
  }
  .header--transparent:not(.header--sticky):not(.header--stuck) .icon{
    fill:  {{ section.settings.transparent_text_color }};
  }
  .header--transparent:not(.header--sticky):not(.header--stuck) .header-cart__bubble{
    background-color: {{ section.settings.transparent_text_color | color_modify: 'alpha', 0.5 }};
  }
</style>


<div class="header__wrapper{% if transparent_header %} header--transparent{% endif %}"
  data-header-transparent="{{ transparent_header }}"
  data-header-sticky="{{ section.settings.header_sticky }}"
  data-section-id="{{ section.id }}"
  data-section-type="header">

  {% if section.settings.header_enable_account or section.settings.header_enable_search or section.settings.header_message != '' %}
  <div class="info-bar showMobile">
    <div class="wrapper text-center">

      {% if shop.customer_accounts_enabled and section.settings.header_enable_account %}
        <div class="header-account-link">
          <a href="/account"><img src="{{ 'account.svg' | asset_url }}"></a>
        </div>
      {% endif %}

      {% if section.settings.header_message != '' %}
      <div class="header-message uppercase{% if section.settings.header_enable_account or section.settings.header_enable_search %} header-message--crowded{% endif %}">
        {% if section.settings.header_message_url != blank %}
          <a href="{{ section.settings.header_message_url }}">{{ section.settings.header_message | escape }}</a>
        {% else %}
          {{ section.settings.header_message | escape }}
        {% endif %}
      </div>
      {% endif %}

      {% if section.settings.header_enable_search %}
        <div class="header-search__wrapper">
          <div class="header-search">
            <form action="/search" method="get" class="input-group search" role="search">
              {% if section.settings.search_only_products %}<input type="hidden" name="type" value="product">{% endif %}
              <input class="search-bar" type="search" name="q">
              <button type="submit" class="btn search-btn"></button>
            </form>
          </div>
        </div>
      {% endif %}

    </div>
  </div>
  {% endif %}

  <header class="site-header {{ section.settings.height }}" role="banner">
    <div class="wrapper">
      <div class="nav--desktop">
        {% include 'nav-contents' with 'desktop' %}
      </div>
      <div class="nav--mobile">
        {% include 'nav-contents-2' with 'mobile' %}
      </div>
    </div>
  </header>
</div>


<script type="application/ld+json">
{
  "@context": "http://schema.org",
  "@type": "Organization",
  "name": {{ shop.name | json }},
  {% if section.settings.logo %}
    {% assign image_size = section.settings.logo.width | append:'x' %}
    "logo": {{ section.settings.logo | img_url: image_size | prepend: "https:" | json }},
  {% endif %}
  "sameAs": [
    {{ settings.social_twitter_link | json }},
    {{ settings.social_facebook_link | json }},
    {{ settings.social_instagram_link | json }},
    {{ settings.social_pinterest_link | json }},
    {{ settings.social_google_link | json }},
    {{ settings.social_youtube_link | json }},
    {{ settings.social_vimeo_link | json }},
    {{ settings.social_tumblr_link | json }},
    {{ settings.social_fancy_link | json }}
  ],
  "url": {{ shop.url | append: page.url | json }}
}
</script>

{% if template.name == 'index' %}
  {% assign potential_action_target = shop.url | append: "/search?q={search_term_string}" %}
  <script type="application/ld+json">
    {
      "@context": "http://schema.org",
      "@type": "WebSite",
      "name": {{ shop.name | json }},
      "potentialAction": {
        "@type": "SearchAction",
        "target": {{ potential_action_target | json }},
        "query-input": "required name=search_term_string"
      },
      "url": {{ shop.url | append: page.url | json }}
    }
  </script>
{% endif %}

{% schema %}
{
  "name": "Header",
  "settings": [
    {
      "type": "image_picker",
      "id": "logo",
      "label": "Logo image"
    },

    {
      "type": "image_picker",
      "id": "logo_mobile",
      "label": "Logo mobile"
    },

    {
      "type":    "range",
      "id":      "logo_max_limit",
      "min":     5,
      "max":     495,
      "step":    5,
      "unit":    "px",
      "label":   "logo width",
      "default": 120
    },
    {
      "type": "link_list",
      "label": "Menu",
      "id": "main_menu_linklist"
    },
    {
      "type": "header",
      "content": "Meganav image"
    },
    {
      "type": "image_picker",
      "id": "meganav_image",
      "label": "Meganav image",
      "info": "500 x 800px .jpg max"
    },
    {
      "type": "url",
      "id": "meganav_link",
      "label": "Meganav Image Link"
    },
    {
      "type": "header",
      "content": "Sticky header"
    },
    {
      "type": "select",
      "id": "header_sticky",
      "options": [
        { "value": "static", "label": "Default header"},
        { "value": "sticky", "label": "Sticky header"},
        { "value": "scroll", "label": "Sticky header only when scrolling up"}
      ],
      "label": "Header behavior",
      "default": "static"
    },
    {
      "type": "header",
      "content": "Transparent header"
    },
    {
      "type": "checkbox",
      "id": "transparent_home",
      "label": "Enable on the home page",
      "default": false
    },
    {
      "type": "checkbox",
      "id": "transparent_collection",
      "label": "Enable on collections",
      "default": false
    },
    {
      "type": "checkbox",
      "id": "transparent_blog",
      "label": "Enable on the blog",
      "default": false
    },
    {
      "type": "checkbox",
      "id": "transparent_article",
      "label": "Enable on articles",
      "default": false
    },
    {
      "type": "checkbox",
      "id": "transparent_page",
      "label": "Enable on pages",
      "default": false
    },
    {
      "type": "color",
      "id": "transparent_text_color",
      "label": "Text and icons color",
      "default": "#ffffff"
    },
    {
      "type": "image_picker",
      "id": "transparent_logo",
      "label": "Alternate logo"
    },

    {
      "type": "image_picker",
      "id": "transparent_logo_mobile",
      "label": "Alternate logo mobile"
    },

    {
      "type": "header",
      "content": "Top Bar"
    },
    {
      "type": "text",
      "id": "header_message",
      "label": "Announcement text",
      "info": "45 characters or less recommended"
    },
    {
      "type": "url",
      "id": "header_message_url",
      "label": "Announcement link"
    },
    {
      "type": "checkbox",
      "id": "header_enable_account",
      "default": true,
      "label": "Show account link in header"
    },
    {
      "type": "checkbox",
      "id": "header_enable_search",
      "default": true,
      "label": "Show search in header"
    },
    {
      "type": "checkbox",
      "id": "search_only_products",
      "label": "Only search products"
    }
  ]
}
{% endschema %}

nav-contents-2.liquid

<div class="mobile-wrapper">
  <div class="header-cart__wrapper">
    <a href="/cart" class="CartToggle header-cart">
      {% include 'icon-cart' %}
    </a>
    <span class="header-cart__bubble cartCount{% if cart.item_count < 1 %} hidden-count{% endif %}"></span>
  </div>
  <div class="logo-wrapper{% if section.settings.logo %} logo-wrapper--image{% endif %}">
    {% if template.name == 'index' %}
      <h1 class="h4 header-logo">
    {% else %}
      <div class="h4 header-logo">
    {% endif %}
        <a href="/">
          {% if section.settings.logo != blank %}
            {% capture image_size %}{{ section.settings.logo_max_limit }}x{% endcapture %}
            <img src="{{ section.settings.logo_mobile | img_url: image_size }}"
                 class="logo--color"
                 srcset="{{ section.settings.logo_mobile | img_url: image_size }} 1x, {{ section.settings.logo | img_url: image_size, scale: 2 }} 2x"
                 alt="{{ section.settings.logo_mobile.alt | default: shop.name }}">
          {% else %}
            <span class="logo--text">{{ shop.name }}</span>
          {% endif %}
          {% if transparent_header and section.settings.transparent_logo != blank %}
            {% capture image_size %}{{ section.settings.logo_max_limit }}x{% endcapture %}
            <img src="{{ section.settings.transparent_logo_mobile | img_url: image_size }}"
                 class="logo--transparent"
                 srcset="{{ section.settings.transparent_logo_mobile | img_url: image_size }} 1x, {{ section.settings.transparent_logo | img_url: image_size, scale: 2 }} 2x"
                 alt="{{ section.settings.transparent_logo_mobile.alt | default: shop.name }}">
          {% endif %}
        </a>
    {% if template.name == 'index' %}
      </h1>
    {% else %}
      </div>
    {% endif %}
  </div>
  <a href class="menuToggle header-hamburger"{% if nav-contents == 'mobile' %} aria-haspopup="true" aria-expanded="false" aria-controls="ariaHamburger"{% endif %}>
    {% include 'icon-nav' %}
  </a>
</div>
<div class="header-menu nav-wrapper">
  <ul class="main-menu accessibleNav" role="navigation" aria-label="primary"{% if nav-contents == 'mobile' %} id="ariaHamburger" {% endif %}>
    {% if section.settings.main_menu_linklist %}
      {% assign main_menu_linklist = section.settings.main_menu_linklist %}
    {% else %}
      {% assign main_menu_linklist = 'main-menu' %}
    {% endif %}
    {% for link in linklists[main_menu_linklist].links %}
      {% include 'nav-item' %}
    {% endfor %}
    <li class="cart-text-link">
      <a href="/cart" class="CartToggle">
        {{ 'layout.cart.title' | t }}
        <span class="cartCost {% if cart.item_count < 1 %} hidden-count {% endif %}">(<span class="money">{{ cart.total_price | money }}</span>)</span>
      </a>
    </li>
  </ul>
</div>