Given what you've said of the situation, and looking over it myself, it looks like trying to get correct numbers out of past reports might be... difficult. It doesn't appear to me that the Philippines would get any massive penalty or advantage from zeroing the stockpile - is that correct?
The 'advantage' is that the Philippines would not be penalized the 17 tons that it is theoretically in the hole. Of course, if one ignored the tonnage placed into the Coron and the Milano, it would convert to a surplus.
Zeroing out the account closes a set of very unbalanced books.