QB Issue Resolution:

Once you send them and then the money clears, there’s really no practical way to change that through QB.

The next checks will over-calculate the straight line taxes like SS and Medicare, but not the withholding taxes. You may want to double those types of taxes up manually to ‘catch up’, depending (probably) on your employee’s wishes.

If an employee will not be paid again this year, that’s a bit of a pickle as they essentially owe you money.  You can in this case enter liability adjustments so that their YTD tax looks right and then try to get the money back from the employee.

Resolution for Issue 'How to I make entries for direct deposit payroll checks that taxes were not held out due to updates not being installed?' available: Yes (Solved).
Source: Intuit Community forum.

How to I make entries for direct deposit payroll checks that taxes were not held out due to updates not being installed?: 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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