Nios IDE only reads the .ptf file created by SOPC builder, check the file and SOPC builder for "64". EPCS64 may be the name you have given to your EPCS chip in the board description file.
Which FPGA device are you using EPCS4 may be too small to contain the hardware image.
You may create the flash programming script .sh by yourself, just edit the one created by the IDE and run it in the Nios II Command Shell (Cygwin). I you do not know what the parameters mean, find and read the manual or run the executables in the shell with a -h option for help.
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