Hello Pratyush Tomar,
I understand your predicament. The easiest way to write the new device tree files to the eMMC would be to edit the Manufacturer Tool’s scripts in order to accomplish this.
Inside the Manufacturing Tool bundle you should have a documentation folder where you will find the Update Command List User Guide. I would recommend starting with the current profile for the eMMC and change the parameters to it just replaces the desired files.
Regards,