I just went through similar issues with my Denon AVR-1909 receiver, when I upgraded from the Verizon Fios VMS-1100 to the new Verizon Fios One VMS-4100 and Fios One Voice Remote.
I was able to enter the diagnostics and user changes menus mentioned in this thread, but did not see any way to defeat the remote's resetting of the input on my receiver, or to change the selected input as needed. Perhaps I just missed them, but . . .
As it turns out, every time you power on the VMS-4100 with the Fios One Voice Remote, it resets the source (input) on your receiver (on the Denon, it resets to the default "VCR" source for HDMI 3). This also "defeats" the "set to last used input" feature of the Denon receiver. I had (for last decade or so) connected my Verizon STB/DVRs to my receiver via the TV/CBL input (which I reassigned on the receiver to HDMI 3).
The HDMI-CEC settings on the new Fios One Voice Remote apparently messed this up, for me at least. In fact, you can even turn the Fios One VMS-4100 on and off at the box itself without affecting the input to your receiver (i.e., the input to receiver will stay at the "last used setting" if you turn the receiver and/or STB off and on again). BUT, if you turn the Fios One STB off/on with the Fios One Voice Remote, it will always reset the input on the receiver (eg, to "VCR" on the Denon AVR-1909).
The solution? I left HDMI-CEC on, but reassigned the receiver's VCR input source to HDMI 3 (ironically, the receiver's default), renamed that source to Fios One and now all is well.