Hi @Water Monster
Welcome to the Sonos Community!
I don’t know why your Apple remote would keep defaulting to IR mode - with HDMI, your Amp is getting the instruction to change volume from the AppleTV itself via CEC on the HDMI link. A better place to get help for why this is happening would be Apple technical support. Maybe a reboot of the Apple TV does this, though I don’t see why it wouldn’t save the setting - have you tried not turning it off (if you even do, that is).
I was going to suggest we program the Amp to accept the IR commands, but our Use an Apple TV remote with Sonos home theater products page indicates that the lack of a mute button may cause problems with this procedure.
Therefore, please unplug your TV, Sonos Amp and Apple TV from power for a minute or so. Turn them all back on and test. If the problem remains, I suggest Apple are the people to talk to.
There may some people here in the Sonos Community who have experienced this, however, and can tell you what to do about it.