Hi @HazemIhab,
I haven't found your previous BIST hard reset issue in any support ticket or community thread.
I understand you see ST_DONE functional reset.
After the reset the clock configuration is reset, so it needs to be initialized.
If you use the RTD drivers, the Clock_Ip_InitClock() function resets all the clocks to a safe state first — which is probably the delay you see if you initialize the clocks in both the Boot Manager and the application.
It can be configured in the Boot Manager only, but you need to make sure the driver enables all the clocks the application needs — in this case the FlexCAN clock.
Also, all the system clocks must match one of the clock options listed in the RM, e.g. Table 156. Option A - High Performance mode (CM7_CORE_CLK @ 160 MHz) (For S32K388/S32K389).
BR, Daniel