If you no longer qualify or become ineligible for the Employment Allowance part way through the tax year, you have to pay back what you've claimed to HMRC in the tax year. You have to reset the "Employment Allowance Indicator" in the Chart of setup as "NO" and report the same to HMRC through the EPS. When you deactivate employment allowance, the next EPS will show the employment allowance status as "No".

Your previous Employment Allowance claim used to offset your employer Class 1 NICs liability will be reversed back and your Employer Payment Record - EPR will be updated with the Employer NIC liability due to HMRC.

Road Map - Edit Employment Allowance Indicator Setup.
Employer/Setup -> Chart of Setup -> Payrun Customisation -> Employment Allowance Indicator Link -> Edit button -> Select "No" -> Click on Save
( 'Employer/Setup' is the button positioned in the tasking zone menu at the top. It is the first button from the left)

Road Map - To E-file the EPS to HMRC
E-Filing RTI -> E-file RTI FPS, EPS, NVR, YTD FPS -> EPS (Employer Payment Summary) link -> 'Claiming Employment Allowance'
( 'E-Filing RTI' is the button positioned in the tasking zone menu at the top. It is the third button from the left)