declare @date_start datetime, @date_end datetime, @shift varchar(3), @duration int

set @date_start = '2016-03-05'
set @date_end   = '2016-03-06'
set @shift           = '123'

select 
EQUIP_IDENT,
STATUS_CODE,
START_SHIFT_IDENT,
START_TIMESTAMP,
END_TIMESTAMP,

CASE 
      WHEN START_SHIFT_IDENT = END_SHIFT_IDENT
            THEN SUM(DATEDIFF(SS,START_TIMESTAMP,END_TIMESTAMP))
      WHEN START_SHIFT_IDENT = @shift AND END_SHIFT_IDENT <> @shift
            THEN SUM(DATEDIFF(SS, START_TIMESTAMP, END_START_SHIFT_IDENT))
      WHEN START_SHIFT_IDENT <> @shift AND END_SHIFT_IDENT = @shift
            THEN sum((select sum(DATEDIFF(SS, (select END_START_SHIFT_IDENT from PLGOK_EQUIPMENT_STATUS_TRANS_GTC2 where END_TIMESTAMP = est2.START_TIMESTAMP and EQUIP_IDENT = est2.EQUIP_IDENT), START_TIMESTAMP)) from PLGOK_EQUIPMENT_STATUS_TRANS_GTC2 est2 where est2.EQUIP_STATUS_REC_IDENT = est.EQUIP_STATUS_REC_IDENT))
END as 'DURATION'
      
from PLGOK_EQUIPMENT_STATUS_TRANS_GTC2  est
where START_SHIFT_DATE between @date_start and @date_end 
and  @shift like '%'+START_SHIFT_IDENT+'%'

group BY EQUIP_IDENT,STATUS_CODE,START_SHIFT_IDENT, END_SHIFT_IDENT,END_TIMESTAMP,START_TIMESTAMP

Cannot perform an aggregate function on an expression containing an aggregate or a subquery.

sum

(select sum(DATEDIFF(SS, (select END_START_SHIFT_IDENT from PLGOK_EQUIPMENT_STATUS_TRANS_GTC2 where END_TIMESTAMP = est2.START_TIMESTAMP and EQUIP_IDENT = est2.EQUIP_IDENT), START_TIMESTAMP)

THEN sum((select sum(DATEDIFF(SS, (select END_START_SHIFT_IDENT from PLGOK_EQUIPMENT_STATUS_TRANS_GTC2 where END_TIMESTAMP = est2.START_TIMESTAMP and EQUIP_IDENT = est2.EQUIP_IDENT), START_TIMESTAMP)) from PLGOK_EQUIPMENT_STATUS_TRANS_GTC2 est2 where est2.EQUIP_STATUS_REC_IDENT = est.EQUIP_STATUS_REC_IDENT))

 THEN (select sum(DATEDIFF(SS, (select END_START_SHIFT_IDENT from PLGOK_EQUIPMENT_STATUS_TRANS_GTC2 est2 where est2.END_TIMESTAMP = est.START_TIMESTAMP and EQUIP_IDENT = est2.EQUIP_IDENT), START_TIMESTAMP)))

Cannot perform an aggregate function on an expression containing an aggregate or a subquery.