As you can see, the following code should always print 2:

if (false) {
    if (false) {
        System.out.println(1);
    }
} else {
    System.out.println(2);
}

Move caret to first false, press Alt+Enter, choose Invert if. Result:

if (true) {
    System.out.println(2);
} else {
    if (false) {
        System.out.println(1);
    }
}

Press Alt+Shift+F to format the code. Result:

if (true) {
    System.out.println(2);
} else if (false) {
    System.out.println(1);
}

Move caret to true, press Alt+Enter, choose Invert if. Result:

if (false) if (false) {
    System.out.println(1);
} else {
    System.out.println(2);
}

Optional: press Alt+Shift+F to format. Result:
if (false) {
    if (false) {
        System.out.println(1);
    } else {
        System.out.println(2);
    }
}

As you can see, the print statement is no longer called.

Setting to P1 as I think this qualifies as "data loss: User's data are corrupted or lost". Using this feature introduces bugs which can be hard to find in more complex code.

Product Version: NetBeans IDE Dev (Build 201602090002)
Java: 1.8.0_71; Java HotSpot(TM) 64-Bit Server VM 25.71-b15
Runtime: Java(TM) SE Runtime Environment 1.8.0_71-b15