TypeSafe config : reference.conf values not overridden by application.conf

Question

I am using typesafe application conf to provide all external connfig in my scala project, but While trying to create shaded Jar using maven-shade-plugin and running it somehow package the conf in jar itself which cannot be overridden while changing the values in application conf.

<plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>${maven.shade.plugin.version}</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <createDependencyReducedPom>false</createDependencyReducedPom>
                            <transformers>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                    <mainClass>test.myproj.DQJobTrigger</mainClass>
                                </transformer>
                            </transformers>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

I am not sure of the behaviour when I am trying to load all configs from the application conf itself. using ConfigFactory

trait Config {

  private val dqConfig = System.getenv("CONF_PATH")
  private val config = ConfigFactory.parseFile(new File(dqConfig))
  private val sparkConfig = config.getConfig("sparkConf")
  private val sparkConfig = config.getConfig("mysql")

}

while CONF_PATH is set as the path where application.conf exist while running the jar.

application.conf

sparkConf = {

  master = "yarn-client"
}
mysql = {

  url = "jdbc:mysql://127.0.0.1:3306/test"
  user = "root"
  password = "MyCustom98"
  driver = "com.mysql.jdbc.Driver"
  connectionPool = disabled
  keepAliveConnection = true

}

so now Even If I change the properties in the application conf still it takes the configs which were present while packaging the jar.