The Working Hours calculation in the Attendance DocType is based on the Shift List Doctype
Presently if multiple Check IN and CheckOUTs are associated with a Attendance DocType and on Submit of teh Attendance doctype the working hours is not updated.
We should decouple Shift and working hours calculation.
Working Hours also can be based on the associated CheckIN and CheckOUT (Probably we can enable a CHECK option to pick working hours from Employee CheckIN even if Shift is not selected)
This will help in non shift OT calculation