文章はほぼ問題ありませんが、シンガポール向けには少しだけ表現を簡潔かつ丁寧に整えると、より自然になります。また、「重要な旅行中に心配をかけてしまった」という表現はやや重く聞こえるので、軽く柔らかくすると良いです。修正版例を示します。
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Dear [Customer Name],
Thank you very much for visiting us from Singapore.
We would like to inform you about your Alipay payment.
Although it appeared as completed on your screen, it did not go through on our system, so we processed the payment again at the store.
The correct payment should be reflected in your account shortly.
We apologize for any inconvenience this may have caused during your trip.
If you notice anything unusual or have any concerns after January 5, please feel free to contact us at any time.
We hope you have a wonderful and peaceful New Year in Japan.
Warm regards,
[Your Name]
[Store Name]
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ポイント
「made by Alipay」より「your Alipay payment」の方が自然。
「important trip」→「during your trip」と軽く。
「properly at a later date」→「shortly」の方が簡潔。