Run wsgen t.Foo2 -wsdl against the following java files:
Foo1.java:
package t;
import javax.jws.WebService;
import javax.jws.WebMethod;

public class Foo1 {
    @WebMethod
    public String method1(String str) {
        return str;
    }
}

Foo2.java:
package t;
import javax.jws.WebService;
import javax.jws.WebMethod;

@WebService
public class Foo2 extends Foo1{
    @WebMethod
    public String method3(String str) {
        return str;
    }
}

generate Foo2Service_schema1.xsd
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<xs:schema version="1.0" targetNamespace="http://t/" xmlns:tns="http://t/" xmlns:xs="http://www.w3.org/2001/XMLSchema">

  <xs:element name="method3" type="tns:method3"/>

  <xs:element name="method3Response" type="tns:method3Response"/>

  <xs:complexType name="method3">
    <xs:sequence>
      <xs:element name="arg0" type="xs:string" minOccurs="0"/>
    </xs:sequence>
  </xs:complexType>

  <xs:complexType name="method3Response">
    <xs:sequence>
      <xs:element name="return" type="xs:string" minOccurs="0"/>
    </xs:sequence>
  </xs:complexType>
</xs:schema>

and a  Foo2Service_schema2.xsd
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<xs:schema version="1.0" xmlns:xs="http://www.w3.org/2001/XMLSchema">

  <xs:element name="arg0" nillable="true" type="xs:string"/>

  <xs:element name="return" nillable="true" type="xs:string"/>
</xs:schema>


method1 is lost in the schema.