So now it works finally.
From Nios Project Context menu select Make Targets... -> Build... (Shift+F9)
Select target mem_init_generate
This will create a hex file called "epcq_controller.hex" in "min_init" folder with small boot loader and your nios app included
Open "Convert Programming File" tool.
If this hex file is not already there, add by click on "Add Hex Data".
Leave "Big Endian" and "Absolute Address".
Select recently generated "epcq_controller.hex".
Click generate, open generated jic file using programmer.
or open following XML cof file with the conversion tool and replace with your files:
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
<cof>
<eprom_name>EPCQ16A</eprom_name>
<flash_loader_device>10CL025Y</flash_loader_device>
<output_filename>output_files/test_board.jic</output_filename>
<n_pages>1</n_pages>
<width>1</width>
<mode>7</mode>
<hex_block>
<hex_filename>C:/Users/Alex/test_board/quartus/software/modulator2/mem_init/epcq_controller.hex</hex_filename>
<hex_addressing>absolute</hex_addressing>
<hex_little_endian>0</hex_little_endian>
</hex_block>
<sof_data>
<start_address>00000000</start_address>
<user_name>Page_0</user_name>
<page_flags>1</page_flags>
<bit0>
<sof_filename>output_files/test_board.sof</sof_filename>
</bit0>
</sof_data>
<version>10</version>
<create_cvp_file>0</create_cvp_file>
<create_hps_iocsr>0</create_hps_iocsr>
<auto_create_rpd>0</auto_create_rpd>
<rpd_little_endian>1</rpd_little_endian>
<options>
<map_file>1</map_file>
</options>
<advanced_options>
<ignore_epcs_id_check>2</ignore_epcs_id_check>
<ignore_condone_check>2</ignore_condone_check>
<plc_adjustment>0</plc_adjustment>
<post_chain_bitstream_pad_bytes>-1</post_chain_bitstream_pad_bytes>
<post_device_bitstream_pad_bytes>-1</post_device_bitstream_pad_bytes>
<bitslice_pre_padding>1</bitslice_pre_padding>
</advanced_options>
</cof>
