The AV receiver will unfortunately automatically switch to the ARC source when powering it and or the TV up out of standby. This is not a fault with either the TV or the AVR and is due to ARC's dependance upon HDMI CEC. The TV detects the AV receiver and sends a HDMI CEC command to it that results in the AV receiver setting itself to the ARC audio source.
You cannot circumvent this behavious, not without disabling HDMI CEC and in turn ARC, not unless you've an eARC enabled Yamaha AVR and TV? You failed to mention the TV ands AVT models you have.
There is a workaround, but that requires the ownership and use of one of Logitech's Harmony remotes, which you say you have.
My rxv-683 has been playing up lately. Locked into circuit protect mode a couple times. Then a few days rest with no power I can manage to power it up again for week or two of mild use. The front LED display is also malfunctioning, showing mumble jumble after a couple minutes. Any ideas??? ––...
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The SCENE command is required because there's no option to set an individual source as part of a Harmony activity. You'd need to assign a source and the desired startup configurations to the associaiated Yamaha SCENE that you intend including in the Hatmony activity. You may also need to adjust the delay before the SCENE command is issued in order to get the timing correct.
I'm basically still using this method with my current Yamaha RXA1080 and LG C9:
and it works.
Note that even if you are not able to program the Harmony correctly then all you need do is select your source on the AV receiver after everythiong is powered up. THis would then switch you from the ARC source to whatever source you selected.