ご回答ありがとうございます。
コードを変更する前はAmazonpay使用時も受注メールは届いておりました。
何かこちらで入れたコピーコードがおかしい可能性はありますでしょうか？
下記が御社の記事をみてコピーして、本番環境にいれたコードになります。
{% capture email_title %}ご購入いただきありがとうございました! {% endcapture %}
{% capture email_body %}
{% if requires_shipping %}
{% case delivery_method %}
{% when 'pick-up' %}
注文の受取の準備が整うと、メールが届きます。
{% when 'local' %}
{{ customer.last_name }}様、ご注文の品を配達する準備を行っております。
{% else %}
{{ customer.last_name }}様、ご注文いただき、誠にありがとうございます。注文の発送準備を行なっております。商品が発送されましたら、Eメールにてお知らせいたします。
{% endcase %}
{% if delivery_instructions != blank %}
<p><b>配達情報:</b> {{ delivery_instructions }}</p>
{% endif %}
{% endif %}
{% endcapture %}
<!DOCTYPE html>
<html lang="ja">
<head>
<title>{{ email_title }}</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="viewport" content="width=device-width">
<link rel="stylesheet" type="text/css" href="/assets/notifications/styles.css">
<style>
.button__cell { background: {{ shop.email_accent_color }}; }
a, a:hover, a:active, a:visited { color: {{ shop.email_accent_color }}; }
</style>
</head>
<body>
<table class="body">
<tr>
<td>
<table class="header row">
<tr>
<td class="header__cell">
<center>
<table class="container">
<tr>
<td>
<table class="row">
<tr>
<td class="shop-name__cell">
{%- if shop.email_logo_url %}
<img src="{{shop.email_logo_url}}" alt="{{ shop.name }}" width="{{ shop.email_logo_width }}">
{%- else %}
<h1 class="shop-name__text">
<a href="{{shop.url}}">{{ shop.name }}</a>
</h1>
{%- endif %}
</td>
<td class="order-number__cell">
<span class="order-number__text">
注文 {{ order_name }}
</span>
</td>
</tr>
</table>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
<table class="row content">
<tr>
<td class="content__cell">
<center>
<table class="container">
<tr>
<td>
<h2>{{ email_title }}</h2>
<p>{{ email_body }}</p>
{% if order_status_url %}
<table class="row actions">
<tr>
<td class="empty-line"> </td>
</tr>
<tr>
<td class="actions__cell">
<table class="button main-action-cell">
<tr>
<td class="button__cell"><a href="{{ order_status_url }}" class="button__text">注文を表示する</a></td>
</tr>
</table>
{% if shop.url %}
<table class="link secondary-action-cell">
<tr>
<td class="link__cell">または<a href="{{ shop.url }}">ショップにアクセスする</a></td>
</tr>
</table>
{% endif %}
</td>
</tr>
</table>
{% else %}
{% if shop.url %}
<table class="row actions">
<tr>
<td class="actions__cell">
<table class="button main-action-cell">
<tr>
<td class="button__cell"><a href="{{ shop.url }}" class="button__text">ショップにアクセスする</a></td>
</tr>
</table>
</td>
</tr>
</table>
{% endif %}
{% endif %}
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
{% assign gift_card_line_item = line_items | where: "gift_card" %}
{% if gift_card_line_item.first %}
<table class="row section">
<tr>
<td class="section__cell">
<center>
<table class="container">
<tr>
<td>
<h3>ギフトカード</h3>
</td>
</tr>
</table>
<table class="container">
<tr>
<td>
<p> ギフトカードの個別のメールが届きます。</p>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
{% endif %}
<table class="row section">
<tr>
<td class="section__cell">
<center>
<table class="container">
<tr>
<td>
<h3>注文概要</h3>
</td>
</tr>
</table>
<table class="container">
<tr>
<td>
<table class="row">
{% for line in subtotal_line_items %}
<tr class="order-list__item">
<td class="order-list__item__cell">
<table>
<td>
{% if line.image %}
<img src="{{ line | img_url: 'compact_cropped' }}" align="left" width="60" height="60" class="order-list__product-image"/>
{% endif %}
</td>
<td class="order-list__product-description-cell">
{% if line.product.title %}
{% assign line_title = line.product.title %}
{% else %}
{% assign line_title = line.title %}
{% endif %}
{% if line.quantity < line.quantity %}
{% capture line_display %} {{ line.quantity }} of {{ line.quantity }} {% endcapture %}
{% else %}
{% assign line_display = line.quantity %}
{% endif %}
<span class="order-list__item-title">{{ line_title }} × {{ line_display }}</span><br/>
{% if line.variant.title != 'Default Title' %}
<span class="order-list__item-variant">{{ line.variant.title }}</span><br/>
{% endif %}
{% if line.selling_plan_allocation %}
<span class="order-list__item-variant">{{ line.selling_plan_allocation.selling_plan.name }}</span><br/>
{% endif %}
{% if line.refunded_quantity > 0 %}
<span class="order-list__item-refunded">返金済み</span>
{% endif %}
{% if line.discount_allocations %}
{% for discount_allocation in line.discount_allocations %}
{% if discount_allocation.discount_application.target_selection != 'all' %}
<span class="order-list__item-discount-allocation">
<img src="{{ 'notifications/discounttag.png' | shopify_asset_url }}" width="18" height="18" class="discount-tag-icon" />
<span>
{{ discount_allocation.discount_application.title | upcase }}
(-{{ discount_allocation.amount | money }})
</span>
</span>
{% endif %}
{% endfor %}
{% endif %}
</td>
<td class="order-list__price-cell">
{% if line.original_line_price != line.final_line_price %}
<del class="order-list__item-original-price">{{ line.original_line_price | money }}</del>
{% endif %}
<p class="order-list__item-price">
{% if line.final_line_price > 0 %}
{{ line.final_line_price | money }}
{% else %}
無料
{% endif %}
</p>
</td>
</table>
</td>
</tr>{% endfor %}
</table>
<table class="row subtotal-lines">
<tr>
<td class="subtotal-spacer"></td>
<td>
<table class="row subtotal-table">
{% for discount_application in discount_applications %}
{% if discount_application.target_selection == 'all' %}
{% capture discount_title %}
{% if discount_application.title %}
{{ discount_application.title | upcase }}
{% else %}
ディスカウント
{% endif %}
{% endcapture %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>ディスカウント</span>
<span class="subtotal-line__discount">
<img src="{{ 'notifications/discounttag.png' | shopify_asset_url }}" width="18" height="18" class="discount-tag-icon" />
<span class="subtotal-line__discount-title">{{ discount_title }}</span>
</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>-{{ discount_application.total_allocated_amount | money }}</strong>
</td>
</tr>
{% endif %}
{% endfor %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>小計</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ subtotal_price | money }}</strong>
</td>
</tr>
{% if delivery_method == 'pick-up' %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>受取</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ shipping_price | money }}</strong>
</td>
</tr>
{% else %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>配送</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ shipping_price | money }}</strong>
</td>
</tr>
{% endif %}
{% if current_total_duties %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>関税</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ current_total_duties | money }}</strong>
</td>
</tr>
{% endif %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>税金合計</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ tax_price | money }}</strong>
</td>
</tr>
{% if total_tip and total_tip > 0 %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>Tip</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ total_tip | money }}</strong>
</td>
</tr>
{% endif %}
</table>
<table class="row subtotal-table subtotal-table--total">
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>合計</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ total_price | money_with_currency }}</strong>
</td>
</tr>
</table>
{% if total_discounts > 0 %}
<p class="total-discount">
割引 <span class="total-discount--amount">{{ total_discounts | money }}</span>
</p>
{% endif %}
{% assign transaction_size = 0 %}
{% assign transaction_amount = 0 %}
{% for transaction in transactions %}
{% unless transaction.kind == "capture" or transaction.kind == "void" %}
{% assign transaction_size = transaction_size | plus: 1 %}
{% assign transaction_amount = transaction_amount | plus: transaction.amount %}
{% endunless %}
{% endfor %}
{% if transaction_size > 1 or transaction_amount < total_price %}
<table class="row subtotal-table">
<tr><td colspan="2" class="subtotal-table__line"></td></tr>
<tr><td colspan="2" class="subtotal-table__small-space"></td></tr>
{% for transaction in transactions %}
{% if transaction.status == "success" and transaction.kind == "authorization" or transaction.kind == "sale" %}
{% if transaction.payment_details.credit_card_company %}
{% capture transaction_name %}{{ transaction.payment_details.credit_card_company }} (カード番号下4桁: {{ transaction.payment_details.credit_card_last_four_digits }}){% endcapture %}
{% else %}
{% capture transaction_name %}{{ transaction.gateway_display_name }}{% endcapture %}
{% endif %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>{{transaction_name}}</span>
</p>
</td>
<td class="subtotal-line__value">
<strong>{{ transaction.amount | money }}</strong>
</td>
</tr>
{% endif %}
{% if transaction.kind == 'refund' %}
{% if transaction.payment_details.credit_card_company %}
{% assign refund_method_title = transaction.payment_details.credit_card_company %}
{% else %}
{% assign refund_method_title = transaction.gateway %}
{% endif %}
<tr class="subtotal-line">
<td class="subtotal-line__title">
<p>
<span>返金</span>
<br>
<small>{{ refund_method_title | capitalize }}</small>
</p>
</td>
<td class="subtotal-line__value">
<strong>- {{ transaction.amount | money }}</strong>
</td>
</tr>
{% endif %}
{% endfor %}
</table>
{% endif %}
</td>
</tr>
</table>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
<table class="row section">
<tr>
<td class="section__cell">
<center>
<table class="container">
<tr>
<td>
<h3>お客様情報</h3>
</td>
</tr>
</table>
<table class="container">
<tr>
<td>
<table class="row">
<tr>
{% if requires_shipping and shipping_address %}
<td class="customer-info__item">
<h4>配送先住所</h4>
{{ shipping_address | format_address }}
</td>
{% endif %}
{% if billing_address %}
<td class="customer-info__item">
<h4>請求先住所</h4>
{% assign isAmazonPay = false %}
{% for transaction in transactions %}
{% if transaction.status == "success" or transaction.status == "pending" %}
{% if transaction.kind == "authorization" or transaction.kind == "sale" %}
{% if transaction.gateway_display_name == "Amazon Pay" %}
{% assign isAmazonPay = true %}
{% endif %}
{% endif %}
{% endif %}
{% endfor %}
{% if isAmazonPay %}
Amazon Payにご登録の住所です。
{% else %}
{{ billing_address | format_address }}
{% endif %}
</td>
{% endif %}
</tr>
</table>
<table class="row">
<tr>
{% if requires_shipping and shipping_address %}
<td class="customer-info__item">
<h4>配送方法</h4>
<p>{{ shipping_method.title }}</p>
</td>
{% endif %}
{% assign transaction_count = transactions | size %}
{% if transaction_count > 0 %}
<td class="customer-info__item">
<h4>決済方法</h4>
{% for transaction in transactions %}
{% if transaction.status == "success" or transaction.status == "pending" %}
{% if transaction.kind == "authorization" or transaction.kind == "sale" %}
{% if transaction.payment_details.credit_card_company %}
<p class="customer-info__item-content">
<img src="{{ transaction.payment_details.credit_card_company | payment_icon_png_url }}" class="customer-info__item-credit" height="24" alt="{{ transaction.payment_details.credit_card_company }}">
<span>{{ transaction.payment_details.credit_card_last_four_digits }}で終わる — <strong>{{ transaction.amount | money }}</strong></span>
</p>
{% elsif transaction.gateway_display_name == "Gift card" %}
<p class="customer-info__item-content">
<img src="{{ transaction.gateway_display_name | downcase | replace: ' ', '-' | payment_type_img_url }}" class="customer-info__item-credit" height="24">
{{ transaction.payment_details.gift_card.last_four_characters | upcase }}で終わる — <strong>{{ transaction.amount | money }}</strong> <br />
    ギフトカード残高: {{ transaction.payment_details.gift_card.balance | money }}
</p>
{% else %}
<p class="customer-info__item-content">
{{ transaction.gateway_display_name }} — <strong>{{ transaction.amount | money }}</strong>
</p>
{% endif %}
{% endif %}
{% endif %}
{% endfor %}
</td>
{% endif %}
</tr>
</table>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
<table class="row footer">
<tr>
<td class="footer__cell">
<center>
<table class="container">
<tr>
<td>
<p class="disclaimer__subtext">ご不明な点がございましたら、このメールにご返信いただくか、<a href="mailto:{{ shop.email }}">{{ shop.email }}</a>までご連絡ください。</p>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
<img src="{{ 'notifications/spacer.png' | shopify_asset_url }}" class="spacer" height="1" />
</td>
</tr>
</table>
</body>
</html>
