Any full bridge driver should already have "flywheel" diodes from the outputs back to the supplies; they are essential for proper operation!
In effect, a full wave bridge that directs back EMF to the DC side.
If the internal device bridge is not adequately rated, you need to add a higher power high-speed bridge of suitable ratings.
You
cannot add diodes between the ECS and generator! the signal there is AC and both directions of current flow are required.
Typical internal circuit for a three phase power stage; this example shows a split supply, but the centre tap is not essential.
The battery charging side needs regulation as well, you cannot only have a rectifier for that.
A good servo drive could be more suitable to control the motor. Servos typically have inputs for both speed and torque, and can actively brake the motor is the setpoint is lower than the actual speed, which returns power to the DC supply, via the internal diodes.
By switching to torque control once the engine started & with a zero-speed setpoint, the current produced by braking could be regulated with an additional feedback circuit (translating battery voltage to torque command) to provide a stable voltage at the batteries, to charge them.
The servo drive and motor would need to be rated to above the maximum possible engine speed (x motor coupling ratio).