@Hyper2020
I don’t understand your problem because it does not make sense as you described.
If you filed the form 941 as required, and you filed form W-2 and W-3 as required, but you simply did not include your employee wages as an expense on your schedule C, that would not block your employees from receiving their tax refunds.
A single member LLC is a disregarded entity and you would file one tax return for the whole year that lists your business and personal income. Your business is listed on a schedule C, and you report your gross income and your expenses and you pay income tax and self-employment tax on your net profit after expenses. If you did not include your business on your personal form 1040, you will file an amended form 1040 that adds the schedule C and all of your business information including your expenses for employee wages.
However, failing to file a schedule C by itself will not block your employees from receiving their tax refunds. You must have failed to do something else. Either they are subcontractors, not employees, and you failed to issue a 1099-NEC, or they are employees and you failed to issue W-2s.
