Assuming you want to use different business calendars by loading different jbpm.cfg.xmls;
When you use a Timer, a scheduler service thread will set repeatDate to the timer using BusinessCalendar which is associated with given jbpmContext. The jbpmContext comes from default jbpm.cfg.xml (jbpm.esb/jbpm.cfg.xml). Also the BusinessCalendar field is static. So you cannot switch business calendars for each Timer in the scheduler service thread.
The timer should be able to acquire the business calendar which was used at the time of Timer creation.