It's still mysterious how you managed to get the protection bits set. Did you or someone else previously use the board with a design involving EPCS programming actions? I don't know the functionality of the NIOS flash tools, they may have additional functions in this regard. Generally I see at least these options:
- Connect a hardware programmer to the EPCS device through the AS connector. EPCS4 is basically compatible to industry standard serial 4 MBit flash, e.g. Numonyx M25P40.
- Desolder the device and put it into a hardware programmer
- Write your own software to control Altera programming hardware. It's easy with ByteBlaster II, but requires knowledge of an undocumented interface with USB Blaster. The USB Blaster hardware can be connected through FTD2XX.DLL directly, but you need to know the commands to control the programming signals.