I just downloaded the US manual from Pioneer's website.
check pages 84 & also 66 in your manual, based on the manual's troubleshooting guide which is there even though you say the manual doesn't mention anything - fyi there's a remote control section in the troubleshooting guide on page 88 or 89.
it's possible the remote control ID number in the receiver setup menu got changed. since the remote can operate up to 4 receivers, which ID number the receiver is set for controls which remote can control it. they need to match. possible it accidentally got changed from wrong menu choices...default setting is 1 so check using steps on page 84 and if it's not 1, change it. make sure the remote ID number in the receiver & the remote are same.
the inputs that can be controlled by the remote are also selectable & changeable so if the above isn't the problem, read page 66 and check those out.
my guess is if both the pio remote and the Harmony don't work, then the receiver's remote control setting may be the culprit.