Hello @Juns
I have reviewed the details you provided, I tried now the "can_pal_S32K118" example available in the SDK 4.0.1 and with the same board, but I did not observe observe the same behavior. Please notice that the evaluation boards are designed to give access to a wide variety of the available peripherals. However, if you are using a custom board with the specific requirements of the application, the example should work properly as well. Therefore, I suggest to try the same example on your side and observe if you notice the same behavior.
About the flashing operation, as Design Studio only provides a way to Flash the MCU by debugging the application, hence the need to open a debug session to do the flash operation.
Also, could you please give me more details of which memory start address you changed? Given that if you changed some flash start address to 0x00000000, you will have issues, since that is the start address of the flash interrupts as shown in the following image:

Please let me know if the example project shares the behavior of your application, and I will be waiting for your answer.
- RomanVR.
Best Regards!