Might seem like a "silly" question but I am assuming that the front panel buttons on the AVR are still functioning as normal? Has there been a recent firmware update to the unit?
Mainstream manufacturers, like Pioneer, will have multiple IR codes for various equipment and I wonder as well, somehow, has this mysteriously changed especially since you stated all other components commands remain intact? Another possible option is in many cases there are a number of ways of re-setting the remote, however, in doing so, it may result in a loss of commands for your other equipment and would require a re-install. What does the manual say about this, if anything?

Other than that, I guess a call to Pioneer is in order. The problem is, like most mainstream manufacturers, trying to get a helpful and timely response from these people can be like "pulling teeth".