Hi David Bayliss,
If you have updated your estimated pay on your personal tax account then your tax code will be adjusted accordingly.
If once updated you have overpaid your tax then when the amended code is operated by your employer any repayment due would come back through your salary.
We would need to access your record to review the tax code.
If you contact HMRC direct we can review this for you.
Income Tax: general enquiries
Thank you.