Cyclone IV and Nios II Firmware Update

The bootloader is encapsulated in the fpga configuration, namely in the sof file.

When you add a epcs controller, the default bootloader is automatically added to the project and built in fpga configuration. You should have a epcs_controller_boot_rom.hex in your Quartus project directory; if I recall correctly this is the default name associated to epcs, but you can change it in Quartus settings or in Qsys.

If you need a custom bootloader you simply change the file and rebuild fpga.

When you regenerate the Qsys component including epcs controller, the hex file is automatically overwritten with the default one. So you must pay attention to replace it with the custom version whenever you change anything in Qsys.