This is an interesting problem. Is editing the stub header file an option? Or is it being automatically generated from the main .h file in some manor?
Since VA is parsing all files in your solution, by design, it is seeing two different versions of the same class, at the same time, in the same namespace. This is going to effect more than just Extract Method. The easiest solution is to "hide" one of the two classes from VA's parser, without effecting anything else.
Adding this to the top of the stub file will get VA to ignore everything that follows it, but since it is also removed by the pre-processor, it won't effect how your code compiles:
// this code hides the rest of the file from VA's parser
// so only one instance of the class is found and worked with
#if 1 == 0