When there is a payroll check in the QB file that didn't actually happen, or in this case the net check was stolen and the wages were not actually earned, this is one of the few cases where it is appropriate to void the payroll check and replace it with a standard bank check.

Voiding the payroll check will unravel all of the employee-based data that drives the W-2 and similar forms.  It will mean that you'll need to amend many of the quarterly payroll forms, some of which QB supports  (like the 941x.)