What is this Fl screen you mention? The AVR's screen? And - why do they make such a 'to-do' on Page7 about 'User Settings'?
Yes, I believe FL they speak of just means Fluorescent AVR display screen.
I don't think they are making an ado about it, but "Cautions" could be changed to notes. The only "Caution" is user settings will be lost and it should default to factory settings.
Notice it doesn't say "only" initialize when X parts are replaced. It's saying that initialization is necessary after X parts are replaced.
As a side note; HDMi inputs and outputs can be finicky as far as passing audio. I've seen them hang many times when trying to play movies and had to cycle power off/on to fix.
If you can, it'd be better to try analog inputs via RCA jacks first before experimenting with digital inputs.
I'm also curious if you can hear anything from plugging in headphones.
Another thing to remember, The AVR audio may be inhibited if inputs and zones aren't defined in the user settings.