QB Issue Resolution:

The person cannot have something deducted Retroactively. You cannot change historic banking or payroll, now; those things already happened, got processed, got reported, etc. Is this Income Tax, or are all taxes missing?

For income tax, tell them to submit 1040ES online at EFTPS. They just need to sign up. Then, they make their own payments if Payroll is not good enough and they never submitted a new W4 to you.

Resolution for Issue 'Employee wants federal taxes to be withheld retroactively (~6 months). How can I do that?' available: Yes (Solved).
Source: Intuit Community forum.

Employee wants federal taxes to be withheld retroactively (~6 months). How can I do that?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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