Thanks for sharing your query here with us, usersam. I can provide details about employment allowances after migrating to Payroll Core.
For Employment Allowances, there's no need to submit a second Employer Payment Summary (EPS) even after the migration to QBO-Core Payroll if you've already submitted these taxes for this month.
However, if you haven't processed them yet, you can submit an EPS in your QuickBooks Core Payroll:
Go to the Payroll section and select Reports (you can find this option within HMRC reporting).
Choose Employer Payment Summary (EPS).
Then, select the tax year you’re interested in and click Run Report.
Now, you’ll see an option to Submit EPS. Choose the tax period you’re submitting for.
Depending on your situation, select the relevant options:
If no payments were made to employees in the current or past pay period and no FPS has been submitted, choose No payments for a period and specify the date.
If there has been a period of no activity, select the Period of inactivity and choose the date.
If this is your final EPS for the tax year, select Final EPS for the tax year.
If the business has ceased, select Final EPS because the PAYE scheme has ceased and provide the scheme cessation date.
Once done, click Submit EPS.
Please note the EPS is cumulative and can only be submitted between the 6th - 19th of each tax month.