Hi,
Have you tried to write "1" to the GDUF_GOCIF[1:0]? Similar action should work for all the flags (e.g. if a desaturation is asserted). Please set a correct "overcurrent action" (GOCAx) to prevent the system from consequent faults (depending on your system requirements).
For your future reference (I understand it's hard to link the information together), please follow the Reference Manual:
Chapter 18.3.2.3 GDU Interrupt Enable Register (GDUIE)
Chapter 18.3.2.5 GDU Status Register (GDUSTAT)
Mainly:
Chapter 18.3.2.7 GDU Flag Register (GDUF)
Chapter 18.3.2.15 GDU Overcurrent Register 0 (GDUOC0)
Chapter 18.4.7 Fault Protection Features
Chapter 18.4.8 Current Sense Amplifier and Overcurrent Comparator
Best regards,
Matej