Finding aggregated values based on dates in another table
Something like this?
SELECT emp.Employee_Id,
       emp.Absence_date,
       SUM(FTE) AS FTE
  FROM #EMPLOYEE_ABSENCES AS emp
  JOIN #employee_Positions AS pos ON absence_date 
                             BETWEEN position_start_date AND position_end_date
                                 AND pos.Employee_Id = emp.Employee_Id
 GROUP BY emp.Employee_Id,
          emp.Absence_date
 ORDER BY Absence_date ASC