You will be allowed to repay the sales tax collected. I have had it done after we filed sales tax. We had to get a refund from the state and then repay the buyer. You definitely are allowed to do that if that is an option.
Going forward, you will need to find a way to keep track of which states passed the minimum requirement and which has not. You will need to work with amazon to in knowing how to set that up so that certain buyers are not tax and some are.
