Qsys can't find hps pin info

Hmmm that's odd. To eliminate Quartus from the mix try compiling a design like this as the top level (i.e. no HPS):

module top (
    a,
    b);
  input a;
  output wire b;
  assign b = ~a;

This will determine if the web version can compile any design that targets an SoC device. If that works then I'm guessing there is a Qsys bug or perhaps the device selected in Qsys doesn't match the device settings for your Quartus project.