Do not file the amended return until you have received the original refund. If it turns out, for any reason, that the IRS changes the original refund, you'll be able to make the adjustment on the amended return. But if you've already filed the amended return you've got a problem.
It's possible that the IRS will notice the error in the estimated tax paid and adjust the original return accordingly, without you having to do anything. Then you won't need to file an amended return.
