Employment Allowance not reported by EPS on Standard Payroll. How do I submit it for the previous tax year?

I am using Quickbooks standard payroll.   Although it was set to claim Employers Allowance for the previous tax year - and the automated journal calculated it correctly, my client has received a demand from HMRC for Employer's NI.  It looks as if an EPC was not generated so I need to submit one through QB to put this right. I am told by support this is not possible?  So how do I put it right with HMRC?