"Our prior accountant recorded the payment using a journal entry instead of the Payroll Liabilities feature so it's still showing past due.  I would like to find a way to delete it from the Scheduled Liabilites list.  There are several line items with the same issue."

JE and regular checks and Bills are always an error for paying liabilities.

You need to look at the account used in the JE, such as Expense or Liability.

Then, you will "reverse" that entry, like this:

Pay Liabilities, for how it should have been done, for each date and those payroll items that should have been that entry. Then, click on the Expenses tab, and using the negative trick here, post to the same account as the JE used. End with a 0 total check. Now the Payroll Liability should be cleared properly and the accounting data looks like this:

Expense or Liability from JE (the error) $x

Your Pay Liabilities correct method = $x

The Expenses tab for reversing the JE entry = -$x