Assuming Alphabet is an array of bool, you're just testing the value of an element of that array. It's perfectly safe -- and it can be done much more simply than what you've written:
if (Alphabet[i]) {
std::cout << A[i] << std::endl;
}
else {
std::cout << A[i];
}
The only values a bool can have are true and false. Explicitly comparing a bool value for equality to true or false is needlessly redundant (and such comparisons can be dangerous in some contexts); just test the value of the value itself. Once you've tested whether it's true, there's no need to test again whether it's false; just use an else clause. If you need to test whether it's false, use the ! (logical "not") operator: if (! Alphabet[i]).
Finally, you're printing the value of A[i] unconditionally, so that part doesn't need to be inside either the if or the else:
std::cout << A[i];
if (Alphabet[i]) {
std::cout << std::endl;
}