http://www.wikihow.com/Avoid-Colloquial-(Informal)-Writing
Napisali tak:
How come – Replace "how come" with "why" in formal writing. In formal speech, you may find "how so" useful. If you find that you are about to use "how come," just use "how so."
How come you ordered steak?
Why did you order steak?
I don’t know how come he ordered steak.
I don’t know why he ordered steak
nie podają żadnych przykładów użycia how so, ale chyba chodzi o krótkie pytania, czyli 'how come?' trzeba zastepować 'how so?'.