Hello samdwyer,
Since reversing and reprocessing the pay run isn't a suitable option for you, there's another workaround to help match the pay run with the bank feed transactions:
- Create a Payroll Clearing Account. Go to Accounting > Chart of Accounts > Create account. If you already have one, you can skip this step.
- Set Up the Account. Create a detail account with the necessary settings as per the screenshot below.

- Allocate Transactions. In Bank Transactions, allocate the separate wage payments to the clearing account.
- Check General Ledger Report. Run a General Ledger Report (Reporting > Reports) to confirm that the payroll clearing account has a debit balance matching the allocations.
- Create General Journal Entry. In Accounting > General Journal, transfer the full pay amount between the bank account and the payroll clearing account.
- Verify the Balances. Run the General Ledger Report again to confirm that the journal offsets the payroll clearing account balance.
Just a reminder, when completing the next bank reconciliation, make sure to reconcile the spend money allocations, the initial pay run and the general journal to balance.
Cheers,
Doreen