It sounds like you did all you could to tell the insurance company about the situation in the first place, so if they now don't charge you appropriately then it is their fault. I wouldn't expect that this would cause a problem for permit renewal, as Mark said, they are not nearly that organized, and even if they do detect it at that time then I would expect that the blame would lie with the insurance company and not with you.
Overall, it appears that the worse that could happen when you renew your permit is that they will then charge you for the insurance between January and May this year, but this seems VERY unlikely. Congratulations on saving yourself some money