How to invert parentheses?

The problem is that after you've changed ( to ), the second if statement will immediately be true, so the character is flipped back again. The reverse isn't true though - if you start off with ) that will be flipped by the second statement, but then it won't be flipped back again. The net result is that all ) characters will be flipped to (, but that's all. So an input of "(((foo)))" would return "(((foo(((.

The simplest way to fix that is to use an else statement:

char[] cArray = text.ToCharArray();
for (int i = 0; i < text.Length; i++)
{
    if (cArray[i] == '(')
    {
        cArray[i] = ')';
    }
    else if (cArray[i] == ')')
    {
        cArray[i] = '(';
    }
}
return new string(cArray);

Alternatively, you could use a switch statement, which would be simpler if you had a lot of different cases to consider:

char[] cArray = text.ToCharArray();
for (int i = 0; i < text.Length; i++)
{
    switch (cArray[i])
    {
        case '(':
            cArray[i] = ')';
            break;
        case ')':
            cArray[i] = '(';
            break;
        // No need for a default as it would be a no-op
    }
}
return new string(cArray);

A switch statement will only evaluate the expression once (on each iteration, of course) so you don't need to worry about the two cases interfering with each other.