Hello there, kdupont.
Thanks for checking in with us. Let's get this sorted out.
Are you using QuickBooks Desktop? If so, once an employee left the company and your QuickBooks is still showing tax payment due, you'll need to pay this liability. Once you issue a check for an employee there'll be a corresponding liability that you'll need pay for.
Here's an article to learn more about this: Scheduled liabilities show as overdue or in red.
I'm always here if you have any other questions with handling payment due for 941 Quarterly Federal Tax. Just leave a reply below and I'll get back to you.