SOPC / NIOS question

If you didn't add the epcs controller, then it was there all along, and the only reason it was NOT in the original symbol was that the previous designer did not update the nios symbol in the bdf.

As for whether you can ignore it, note that Quartus treats the nios symbol like any other device. It doesn't care about unused outputs from a symbol, and it only cares about unused inputs if they are required for something that ultimately drives a signal. In all likelihood, it will delete all this stuff during the minimization process, as long as you don't set some compiler option that prevents full minimization.