You probably get this error, because you did not programmed the board, with the software. You always need to make sure, that the system is up and running, before you trying to connect to the debug cores.
The debug_nets.ltx is located in the following directory: fmcomms1/<carrier>/fmcomms1_<carrier>.runs/impl_1/
You can open a hardware manager, connect to the board, let the tool throw an error, after that define the corresponding ltx file and refresh the device.
This thread starting to get too big, please open a new thread at the FPGA Reference Design community, if you have any other questions.
Thanks,
Istvan