After all it's already a hack job in the hangar...
So... Maybe this shield generator isn't really hooked into the flux grid properly anyway.
It works fine in the hangar, but when stressed it can't really cope well at all and shuts down violently.
Game effect:
Ships with a makeshift shield cannot be overloaded by shield flux. When the flux hits maximum, the shield will instead 'fail' and take some amount of time to reset before it can be raised again. (Marked by a countdown in the status area.)
This 'failure' causes EMP arcing based on the maximum flux level of the ship that may temporariliy disable weapons or engines. Larger ships will be more affected than smaller ones.
Adding capacitors to a ship will give it more shield 'HP', but potentially see it suffer more consequences in battle.
HullMods and skills that boost repairs and EMP hardening can mitigate this.