Duplicate Employee on HMRC systems caused by RTI interface problem

My client has a problem with a duplicate payroll record on HMRC which is causing their PAYE record to show incorrect amounts due. This has been caused because Clearbooks (I am told) does not send the employee payroll number to HMRC as part of the FPS. However HMRC use the payroll number as a unique identifier. Their guidance at https://www.gov.uk/guidance/what-payroll-information-to-report-to-hmrc#employee-information says:

"You can assign payroll IDs to your employees. The ID must be unique. Use a different one if you re-employ someone (if you do this within the same tax year restart their year-to-date information from ‘£0.00’) or have an employee who has more than one job in the same PAYE scheme. If you reuse a previous payroll ID you’ll create a duplicate record and report payroll incorrectly."

All my client did was to add a middle name to an employee, that was enough to trigger a duplicate because HMRC assumed this was now a different person! Had the employee's payroll number been sent with each FPS this would not have happened.

Removing the duplicate is proving a nightmare, with both the Employer and Employee helplines saying they are unable to make changes, we have to do it through our software! That appears to be impossible too, as we do not have a duplicate employee in Clearbooks.

Firstly I think Clearbooks should consider making the employee payroll number field compulsory. Secondly I'd be interested to hear if anyone else has had this problem and how they have managed to solve it?