entitymanagerfactory is closed after refreshing ConfigurableApplicationContext - spring

Question

I'm building a web application using Spring MVC. I've been trying to come up with a way to customise some system properties and reload the web application without restarting the Tomcat server.
Currently, I'm doing this task by using refresh() method in ConfigurableApplicationContext and its working at the moment.
#Autowired
ConfigurableApplicationContext configurableApplicationContext;
..
public void reloadConfigurations() {
configurableApplicationContext.refresh();
}
However, if the user logs out after refreshing the system, then after that he will not able to login to the system again.
Here's the message I get as SPRING_SECURITY_LAST_EXCEPTION :
entitymanagerfactory is closed; nested exception is
java.lang.illegalstateexception: entitymanagerfactory is closed.
Can't see any other errors in system logs or tomcat log.
Here's the code
application-cotext.xml
<bean id="mysqlDataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource">
<property name="driverClassName" value="com.mysql.jdbc.Driver" />
<property name="url" value="${jdbc.url}"/>
<property name="username" value="${jdbc.username}"/>
<property name="password" value="${jdbc.password}"/>
</bean>
<bean id="entityManagerFactory"
class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean" destroy-method="destroy">
<property name="dataSource" ref="mysqlDataSource" />
<property name="persistenceUnitName" value="myAppMySql" />
<property name="packagesToScan" value="com.myApp.model" />
</bean>
<bean id="transactionManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<property name="entityManagerFactory" ref="entityManagerFactory" />
</bean>
persistence.xml
<persistence-unit name="myAppMySql" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>
<class>com.myApp.model.SystemConfig</class>
<class>com.myApp.model.User</class>
<properties>
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQL5InnoDBDialect"/>
<property name="hibernate.hbm2ddl.auto" value="update"/>
<property name="hibernate.show_sql" value="false"/>
<property name="hibernate.connection.pool_size" value="5"/>
<property name="hibernate.c3p0.min_size" value="5"/>
<property name="hibernate.c3p0.max_size" value="10"/>
</properties>
</persistence-unit>
Any ideas?? Thanks in advance