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I would like to confirm that £ 3531.50 has been paid to your account by Basc ( Three days payment ) Unfortunately , I couldn't do Same Day Payment without my manager who is not here this morning . I hope you are Ok with it . Cloud you please send me the credit note as soon as possible

if it is any problem with it , please do not hesitate to contact with me
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It is easily understandable, but can be improved, Laventa:

"This is to confirm that £3531.50 (three days' payment) has been paid into your account by Basc ['BASC'?] Unfortunately, we were unable to specify Same Day Payment because of our manager's absence today. If this arrangement is satisfactory, could you please send us the credit note as soon as possible?

If you have any concerns, please do not hesitate to contact us."

In business communication, we represent the company, so usually use the plural pronoun unless a personal relationship has been established.
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Hello Laventa

I think that should be BACS, not Basc.

("BACS" means Bankers Automated Clearing Services.)

MrP
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Comments  
This is great 1 - Thank you very much
I would write it this way:-

"I would like to confirm that £3531.50 has been paid/credited/transferred to your account by Basc ( Three days payment ). My manager is not in this morning so I could not utilize "Same Day Payment". I hope that is OK with you. Could you please send me the credit note/RECEIPT as soon as possible?
Should there be any problem/s with this transfer, please do not hesitate to contact/notify me."
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 MrPedantic's reply was promoted to an answer.