Welcome to the forum! I thought that it might be that you were accidentally toggling between the digital and analog inputs, and your second post makes me think that even more.
To test this, go to the front panel of the Pioneer behind the flip-down door and press the "SIGNAL SELECT" button until the LCD reads either "Auto" or "Digital" (because you are using the digital inputs). If that gets your sound back, then we know what the issue is - then we just have to figure out what on the new remote is causing it.

Btw, I think that you need to select the input signal type on each input.