I think the answer has been given already. There's a maximum amount of debt, based on difficulty, that has nothing to do with the -500bc.
That number on his difficulty is -2000 BC. In other words, if you spend 75000BC upgrading a fleet of large ships, and click TURN, on that difficulty level, your debt will be reduced to -2000 automatically, whether or not your empire is turning a weekly profit or defecit.
Okey dokey.