Problem with updating memory initialization file in Quartus for the Application.hex bootloader

After the power cycle the factory image is configured and then the nios boots correctly. When I configure the application image without the application hex file, the sof is configured properly. I checked it by using PIO in Qsys and assigning different values to the fpga pins. In the factory configuration the fpga pin has 3 volts and in the application image it has 0 volts. I was also able to download elf file on the application image from eclipse.

There is however one big problem , the nios in applicaiton image does n't boot when the application hex file is loaded. The problem is likely due to the fact the epcs bootloader which I am using starts from address 0 in the EPCS and is not able to find the proper hex file for the application image and the factory image is loaded again after the reconfiguration code is executed.

I replaced the epcs_boot_rom.hex inside my project with the .hex file having the same name which I created from a custom bootloader.

The problem is that the replacement does n't work and the default bootloader is loaded again. When I try to update the memory initialization file I get the following error: