Are you suggesting that the HDMI audio input might not be correctly assigned after clearing the "microcomputer" with the power button hold type of reset?
For that matter, pushing and holding the power button is named on page 156 and again on 157 of the manual as the means of rebooting the receiver. Does this accomplish something different from the Reboot command in the network type commands?
A good answer is easier with a clear question giving the make and model of everything. "The biggest problem in communication is the illusion that it has taken place." -- G. “Bernie” Shaw