The allocation of paid fuel (or fuel benefit) for an employee is part of the car assignment - so if an employee has decided to 'hand in' their fuel car from a certain date and stop receiving the benefit, you need to withdraw the car and the fuel, benefit and the provide the car again from the next day without that benefit assigned.
To accomplish this, find the employee in question, and view the current car allocation - in the example below the car is currently allocated all year, and has paid private fuel (fuel benefit) applied:
We then edit the car allocation to withdraw the car on the selected day (say 16th May) and click Save:
We then nee to provide the same car again from the next day (the 17th of May), but without the fuel benefit applied:
The employee now has a car running up to May 16th including fuel benefit, and another from the 17th of May excluding the fuel benefit.
This will then mean a person's P11D document will list 2 car allocations and not use the Fuel Withdrawn tick box.
Extract from form P11D highlighting tickbox (not used)