Hi Daniel,
As mentioned in below point, to re-enable the operation first the GDU and then PMF fault must be cleared.
1.13.3.4 Static Timing Fault Handling
The following Faults and/or errors can occur:
• Desaturation error, Overvoltage, Undervoltage, External fault
The application run-time error is handled by the GDU without CPU interaction. Firstly the FETs are
disabled and the PMF signals switched to an inactive state. To re-enable the operation first the GDU fault
and then PWM fault must be cleared, to automatically re-enable the FET driving at the next PWM
boundary
We have referred the MC9S12ZVML128 hall sample code for our application development.
We have done the PMF setting as below,

In SW, we have cleared the GDU flag and handled the PMF fault on GDU level(i.e. GDU over curent, VLS under voltge, HD over voltage failsafe are implemented) and its respective GDU flags are cleared.
As per the datasheet, clearing of PMF fault is must.
Request you to confirm that, is it ok if we clear the GDU flags and not clearing PMF fault using PMF register?