When the Three Great Empires wanted to write off the accounts, it meant they no longer wanted the money. They would treat it as part of the Interstellar Council's budget. Neither principal nor interest needed to be repaid, as if none of it had ever happened.
As for why things had turned out this way, it had to be mentioned that although the Interstellar Council had been established jointly by the Three Great Empires, they were not a unified polity. The relationship between the Skrull Empire and the Kree Empire was practically modeled after Britain and France, except the Hundred Years' War had become the Thousand Year War. The two were mortal enemies, yet both looked down on the Shi'ar Empire.
The Kree Empire and the Skrull Empire no longer wanted war and needed time to recuperate, while the Shi'ar Empire did not want those two keeping an eye on it. So the three of them reached an agreement and established a "United Nations."
But even on Earth, everyone tried to manipulate the United Nations and turn the situation to their own advantage. How could the Three Great Empires possibly refrain from doing the same?
Thus, when the Interstellar Council handled interstellar affairs, situations like this arose: something clearly happened within Kree territory, and the Supreme Intelligence should have sent troops to handle it, yet he refused. He insisted on making the Interstellar Council deal with it instead.
The Interstellar Council needed money to solve problems, and money meant budget funds. That was the Supreme Intelligence's goal: I already spent money to provide you with a budget, so naturally, I had to use the portion I paid for myself. Even if I did not use it, I could not let my enemies use it. So I had to use it