The default location for Qsys on-chip memory .hex files is <qsys_top_filename>/sythesis/submodules/<qsys_top_filename_onchip_memory>.hex
After generation of the Qsys design, you can find the Qsys on-chip memory .hex files located in the directory above.
However, if you wish to use the non-default initialization .hex file, please make sure that you have selected the correct .hex file and added the correct include / library path in Quartus II.
For memories containing pre-initialized Nios® II code you can create a .hex for the memory by running mem-init-generate.
To run mem-init-generate right click on the application folder in the Nios II SBT4E (Nios2 Software Build Tools for Eclipse) and select Make Targets/Build/mem-init-generate. A mem-init subdirectory will be created in the software directory with the appropriate .hex files.
We recommended adding the file <software project directory>/mem_init/mem_init.qip from the software project into the Quartus project. The .hex file(s) will then be automatically detected on a quartus compile.
Alternatively the generated .hex files can be copied to the <qsys_top_filename>/synthesis/submodules/ directory to replace the default ones there. Note: Running Qsys generate will overwrite these .hex files, replacing with the default content.
This information will be included in a future version of the Nios II Documentation.