You may try to Flash your board using programming scripts directly from the cygwin shell.
The script can be found in (since the script was probably not yet created for your project try one from the demo projects for the development board):
...\quartus_project\software\software_project\Debug
Modify the script and run it, if you do not know what command parameters mean do
nios2-flash-programmer --help
You may omit checking of sysid or place --accept-bad-sysid in the scripts to avoid errors...
But this might not solve the problem, try starting a new project from scratch:
- start a new Quartus project with the same pinout definitions (they can be found in the .qsf file)
- start a new sopc project
- create a new board description from the sopc menu (the epcs flash can be called anything, U1 does not seem to appropriate)
- select the board description
- select only some essential components (cpu, memory, epcs, a timer)
- generate the sopc project
- in quartus connect SOPC IO signals with chip pins
...
Be sure to use a slightly different name for the quartus project, sopc project and board description.
Learn to compare source files, this is a list of source files for a simple hardware project, all other files are generated or copied from libraries.
my_project.qpf (nothing useful, only project definition)
my_project.qsf (specifies the chip, pinout, ... can usually be safely modified in a text editor)
my_project.bdf or my_project.vhd (top level project source file)
my_sopc_project.ptf (description of the SOPC builder component)
/my_project_board/class.ptf (board description, did you check this?)
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