Why wouldn't it be "Lis-tu une lettre?"
"Lis-tu" would be a more formal way.
Thanks, good to know I am thinking correctly.
If "Tu lis une lettre?" is "Do you read a letter?", inquisitive, what would be "You read a letter", declarative?
Put otherwise, what, if anything, indicates that this is a question, besides punctuation and inflection?
Nothing. Punctuation and inflection (and context in some cases) would be the determinant for whether it's a question or an affirmation.
how can you tell lit from lis in the audio
I believe it is just knowing that it's Tu lis, je lis, il lit, elle lit type of thing. I can't hear any difference.
I can't recognize "une" in this audio
There are definitely issues with the way that the audio relays on this site; there are many words that are very vague to distinguish, if you can hear them at all.