Historic Penalties and interest 3 years from 2014/15

I took on a new client who had previously been employed but recommenced SE in 2023/24. His SA account was showing clear prior to commencement. I completed the tax return early in April and client was due a refund in excess of £3k, unfortunately unlike a lot of my early submissions this was not repaid but showing as due to him. Hours on the phone to be told it was being referred and to call back etc. I have logged in daily to check with no movement, same overpayment showing as due, until this morning when it had vanished. Excited I thought the repayment had been issued, but nothing in the repayment section. Went to tax options and it now appears that HMRC have applied maximum penalties and interest for tax years ended 2015/2016/2017, effectively wiping out the entire £3k+ refund EXACTLY? No other liability left? The penalties and interest are all dated 24/4/24, so had never been previously applied and presumably client never been notified. Can this be appealed? What are my options?

Hi Paddy Kelly,
The tax years quoted are most likely years the taxpayer was due to file a tax return for, but remained unfiled, and which we were then unable to contact the taxpayer about.
When the taxpayer reopened their record, the oustanding years will have been reactivated, and the penalties you now see calculated.
To confirm this, and to allow us to correctly advise you on how to proceed, we would need to access your client's record.
Contact us by webchat or phone here:
Self Assessment: general enquiries
Thank you.