Earlier quoted context omitted.
Just let the plaintiff or prosecuter decide what evidence they would have liked to find and instruct the jury to assume it was found. This would never happen again anywhere.
This seems like some insane government overreach, though. Like, make the penalties for destroying evidence super steep and criminally liable sure, but it seems pretty wild that you could be convicted of a crime without evidence. In that case, the government has an incentive to destroy evidence and its paper trail.
(If you mean "Has the government failed to meet its burden of disclosure regarding evidence in its possession:" yes, it occasionally happens. The significant incentive against it is that it's immediate grounds for a mistrial and incredibly embarrassing to a prosecutor's office that has it happen on their watch).