" I still get $3.99 for the old inventory and international shipping cost."

There are multiple templates on the site.

First, go into the template that Amazon shows you are using for that order. Then open THAT template and see if you have your settings correct at this time.

For OLD ASINs Amazon does NOT automatically update listings to a newer shipping template. I have listings out there with probably 20 different templates that I just have not taken the time to switch around so far.