Hi,
You say "smoothly break" .. but the you say "short circuit".
But "short circuit" is "hard breaking", not smooth breaking...
Instead of hard short circuit, you could use PWM.
Depending on your circuit this could be:
* PWM = 0: all switches are OPEN
* PWM = 1: all lower switches are ON
Then smoothly increase the duty cycle until the motor stops.
Mind: the rotating energy is pushed back as electrical energy to the bus voltage capacitors.
This means the voltage will increase! You should include some overvoltage protection.
Klaus