the 100A fuse is a back-up when the power limiting Printed Circuit Board (what you call the Protector) is out of order. In order to connect this fuse, you need to remove both wires from the PCB (just pulling down) and connect them to the 100A fuse.
There seems to be a mechanic problem in the boom gear-box. And therefore, the PCB allows the motor to run for a few seconds, then cuts off power because of too high amperage (that's what it's designed for).
If you connect the back-up fuse, you may blow it within some seconds too because the mechanic resistance is too high, making the amperage rise above 100 A (you may also burn the wires too!!).
It seems that you need to take down the gear-box and open it to check the worm gear and the bronze "teeth wheel".
If you can't find a good skilled mechanic where you are, you may think of just replacing the gear-box (I don't like when you say the shaft went out of the gear-box...).
Good luck and remember to never hit the track end stopper with the traveller. This definitely kills the gear-box after several knocks.