After you have your problem repaired(whether it be A/C or Heater Core)and you've cleaned it and still have the smell the mildew has set up in your padding of your carpet. you will have to take the carpet out and turn it over(where padding shows) and steam clean it and let sun dry complety....just finished one yesterday with same problem you're are having its very time consuming but its the only way to rid it of the mildew and the longer it sits in the carpet to harder to come out....hope this info. helps.