Since jboss 4.0.4.GA (see JBAS-1091) ejb timers can be persisted at undeployment time.

However, this was a feature added to the org.jboss.ejb.txtimer.EJBTimerService API with a second removeTimerService method:

/**

• Remove the TimerService for a given containerId.
• This should be used to remove the timer service and timers for
• any type of container (session, entity, message) at the time of
• undeployment.
  *
• @param containerId The string identifier for a class of TimedObjects
• @param keepState Flag indicating whether timer persistent state should be kept or removed
  */
  void removeTimerService(ObjectName containerId, boolean keepState) throws IllegalStateException;

EJB3 uses the old removeTimerService() method that has the legacy behaviour of removing the timers at undeployment time.
void removeTimerService(ObjectName containerId, Object pKey) throws IllegalStateException;

So, call the new method instead. However, this will mean the EJB3 bundle will only run on JBoss4.0.4+