Debugging the Hardware fault

I'm a little confused. You say you cannot program the FPGA via JTAG. However, "1 LED blinks". Is it one of D10-D19? If so the FPGA is clearly doing something. Or is it another LED? Which LED is blinking?

If your power rails are all good but you can't program the FPGA via JTAG, then it doesn't look good for your FPGA - especially if the board was previously working. You should always be able to reprogram the FPGA via JTAG.

You won't be the first to fry your FPGA without knowing why. I see you've put quite a bit of protection into your design. Are you being careful with your handling of your board?

Cheers,

Alex