@digilog
You need to distinguish between peripheral configuration (here, the GPIOs) and execution contexts.
If your GPIOs are already configured by the FSBL, they will be directly usable in the Application, and you will have nothing to do except HAL_GPIO_WritePin in the Application, just like SystemClock_Config() which is executed by the FSBL, the RCC configuration remains intact in the Application.
Remember that the STM32N6 is always in secure mode.
However, if you have a third execution context, Non-Secure (AppNS), this is different, and you will need to configure the peripheral privileges in the secure world in order to use them in the non-secure world (refer to the Template_Isolation_LRUN example)
Let me know if it clarifies your question ?
Best regards,
Romain
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