NIOSII Boot Configuration with EPCS and JTAG-SFL

The --device=EPCS128 isn't actually relevant, I've seen it used on all EPCS devices. I think Altera should just rename it to --device=EPCS ;)

Looking at your log I see a more interesting error:

Info: Reading System ID at address 0x00022080: 
Info:     ID value does not match: read 0x0000000D; expected 0x00000013
Info:     Timestamp value was not verified: value was not specified

This indicates that the image currently in the FPGA isn't what the programmer expects. As it is still trying to flash the EPCS anyway, it probably means that you disabled the system ID check in Eclipse. This isn't recommended. If the the system ID check is enabled, when you have a system ID error then you will just get an error message and the flash programmer will stop, which is better.

So now you need to figure out why you don't have the expected image. You need to be sure that the .sof image currently in your FPGA corresponds to the .sopcinfo file that was used to generate the BSP. Each time you do a change in the QSYS/SOPC builder system, after regeneration you need to recompile the Quartus project and regenerate the BSP. Then upload the new .sof file to the FPGA and you can use the Nios flash programmer.