I have attached a capacitor and a pull up resistor on EN line. GPIO0 is also pulled to GND during flashing the code. Please see the attached rough schematic of my system and timing diagram for more information. I have jumped my EN and GPIO0 line from board to a breadboard where I am manually jumping the EN & GPIO 0 wires to GND. This is just to be sure that I am pulling down the signals while booting and there is no noise or sudden voltage fluctuation while toggling the signals.
For extra precaution I have also pulled up or pulled low other strapping pins as shown in schematic.
While uploading the code I pull down first GPIO 0 line and then EN line to GND and later when I see
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'Connecting........_____'
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'A fatal error occurred: Failed to connect to ESP32: Timed out waiting for packet header'
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'rst:0x1 (POWERON_RESET),boot:0x3 (DOWNLOAD_BOOT(UART0/UART1/SDIO_REI_REO_V2))
waiting for download'