Bypass diode 1N5400 series on 48v system
Fuses

Fuses are used as a last resort measure to prevent fires. They should be able do completely disconnect the circuit.
Pay some respect to fuses and Don't shunt them with anything.
Your design should not rely on the fuse blowing at some point in order to work correctly.

The relay (contactor)

I think you should not expect the contactor to disconnect in case of a regenerative braking. Except if you have a complex and profoundly broken logic that controls it. So no diode needed.

The diode.

If you still want some diode to protect you from currents generated from regenerative braking, you may want a diode that handles the full power of the motor. With some safety margin. 1N54xx diodes are rated for 3A. They are also rated for 200A, 8ms impulse. Is your regenerative braking that short? What about running downhill? You may want a way bigger diode.

The regenerative braking voltage

A permanent magnet DC motor can generate more or less the same voltage that is used to run it to the same speed. Your controller may or may not be able to boost the generated voltage to a value higher than its own voltage rating. I would check if the controller needs protection in the first place.