It seems stupid that once this happens, you can't accept the alert and run tests inside the API Test Tool in production mode, now I know this is showing me the same error as I would have seen if called it, but there should be a way to test while this limit has been hit. Before any one shouts about sandbox.. sandbox is fine if you have enough data to work with so you can work out what is causing the limit to be hit.
Why can ebay not introduce the same logic as google. 25000 has to be exceed for x numbers of days in a row for the $4 charge per 1000 requests. have an application alert you are over the limit, which will then give people a chance to fix it before it becomes a problem. This hard limit is just not funny.