Axis and Axis2 are significantly different, and can almost be considered different technologies. There are certainly different implementations.
That said, the decision to mix them in a single distributed application is questionable. The best route to repair this is to
remove the Axis2 components from the "same lib folder" which contains the Axis stuff.
If you are migrating to Axis2 , you should set up a separate evironment for this new code and only use the new Axis2 material here. Do not mix JAR files or artifacts of both implementations.