How to modify all occurrence of the extracted variable?

In the variable extractor panel you have an option called "Value is encoded". If you choose the custom item in the drop down list you can edit a Javascript in order to modify your extracted value on the fly.

I guess in your case you can use a replace method to automatically replace all your ref: by ref:A strings.

Example:

function decode(encodedValue) {
    var decodedValue = encodedValue.replace(/ref:/g, "ref:A");
    //Apply decoding logic here.
    //JS Libraries can be used
    return decodedValue;
}