Largely inconsequential.
The article is not very clear. The money that is not accounted for is $62.4B. The reason that money is unaccounted for is because of trillions of dollars of accounting adjustments in budgets.
That trillion dollars figure is just summing up the magnitude of all accounting adjustments throughout all the records of the DoD. The moral equivalent of:
SELECT SUM(ABS(trans_amount)) FROM transactions WHERE trans_type = 'Adjustments';
In an imaginary accounting DB. The $62.4B figure was the same thing minus the "ABS()"...