<antcall> will not override existing references, even if you set inheritRefs to true. As the called build files is the same build file as the calling one, this means it will not override any reference set via an id attribute at all. The only references that can be inherited by the child project are those defined by nested <reference> elements or references defined by tasks directly (not using the id attribute).
Inherited references are not available to top level tasks of the child project.