That's exactly what happened to novelist and blogger Richard Lawrence Cohen recently. His post reacting to the email is interesting. I found it, as another commenter on Cohen's site put it, "weird" and wrote this [I've edited out my mistakes]:
Years ago, someone I knew who was entering the field of pastoral counseling as a specialty started asking people that question. "How are you...really?" makes the asker seem so wise, so knowing, so perceptive, so capable of peering beneath the veneers we all put out before the world...especially to those we use to fend off the faux-wise snobs who want to use the people around them to prove their worth. (Which, truth be known, they doubt. But they only become aware of that years later after they've gone through therapy.)
I'm not putting your friend in that category, mind you. But it seems to me that a good 90% of the time, the question, "How are you really?" isn't the genuine query of someone who cares about you and perceives some secret torture dogging your soul. They're people out to glorify themselves. To them, you're the students' cadaver in the medical college surgical theater.
Merle Miller's warped and probably inaccurate oral biography of Harry Truman contains a section about an interview Miller allegedly conducted with a cousin of Truman's. The woman was giving Miller a sense of what life in Independence, Missouri, the President's hometown (and hers), was like. "When I ask people how they're doing, I most emphatically don't want to know the answer," she said. I suppose that's true for most of us. So, it's possible that your friend was asking a question to signal that she or he wanted a friendship composed of more than pleasantries. But, given that the email contained all of one line, I'd be suspicious of that were I in your shoes. I'd wonder if the question weren't more about her or him than you.
Besides, there really is something to be said for maintaining relationships built on pleasantries. Who has the energy or the inclination required to have every friendship be composed of deep soul-to-soul honesty? It's not practical or possible.
Given that reality, it's probably okay that while not being dishonest with others, we not tell each other "how we are...really" every time we're asked.
Pleasantries have their place. The mother of another Democratic president, Jimmy Carter, was asked during the 1976 campaign if her son always told the truth. Miss Lillian allowed as how Jimmy may have occasionally told little white lies. The reporter interviewing her asked what an example of a white lie might be. "Well," she replied, "do you remember how when you came in here and I told you that it was nice to see you?"