When you use setFlags you are replacing the old flags... when you use addFlags you are appending new flags. Remember, a flag is just a integer which is power of two... in binary, flags look like this: 1, 10, 100, 1000, etc... (which in this case are 1, 2, 4, 8). So, what addFlags does is appending the integer you pass using the | operator.

// example... 
// value of flags: 1
intent.setFlags(2|4); 
// now flags have this value: 110
intent.addFlags(8); 
// now flags have this value: 1110