The bothering sentence is: “Custom duties fees for the 99 boxes” The document is only about this 99 boxes, no other quantities are mentioned, in other line above this sentence is written “Missing 99 boxes in container”. So no need to highlight this boxes as it is clear we are speaking only about the same boxes. Please advise with rules
Using the definite article, the writer is speaking about a specific or certain object:
Custom duties fees for the 99 boxes
means reference to a specific collection of 99 boxes that the custom duties apply to, as opposed to
Custom duties fees for 99 boxes
refers to any collection of 99 boxes.
In the second sentence:
Missing 99 boxes in container
The emphasis is that boxes were not in the container and were missing, it could be rephrased:
The 99 boxes were missing from the container
However, to change the used sentence to
Missing the 99 boxes in container
would be a bit awkward.