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I didn't see you are well.

Hi merdogan, I'm sorry, but your suggestion has a complete different meaning.
"I didn't see you are well" means that "Although I didn't see that, you are well."

I think the line means that the person noticed the addressee is not well, doesn't it?.

Hi lilian,
This text can have two meanings.
One of them is " I didn't see you good" or
"your health is not well".
I prefer the last one.

Neither of them is correct in English. I'm sorry.
Thanks anyway.

"You look rough" might be even better.
but.. that might not be what the writer meant, and the meaning is almost the same.

She looks rough! Has she been up all night? Elle n'a pas l'air bien! Elle n'a pas dormi de la nuit?
http://dictionary.reverso.net/english-french/rough

Dear lilian
The Turkish text says " I saw that your health isn't well."

Non hai un bell'aspetto.