i have a little workaround to get a valid EPCS file for updating boards out in the field.
I use my board at the lab, which is equipped with a jtag connector and a RS232 port, program it, using the NIOS 2 IDE flash-programmer. Then i wrote a little c-program, which dumps the EPCS content to the RS232 port. I simply use the run feature of the IDE to transfer it to the target, overwriting the main application in ram. A terminal program is used to save the output, which is formated as iHex file, in a file.
Thats it - it is not perfect, but it works for me...