It seems easy, I'm not sure to understand weel but try this:
Select distinct SegmentID,Sum(distance) as TotalDistance from [dbo].[tblBookingContent]
where Orgnization = 'REGERINGSKANSLIET'
and (segmentid is null or segmentid in ('LUX001S02','LUX001S11','SWE001S03','SWE001S09','SWE001S14','SWE001S20','SWE001S15','SWE001S23'))
and IsV4 in (0,1)
and departuredate between
convert(datetime, '2016-07-01', 110) and
convert(datetime, '2016-09-30', 110) and MPSS= 1
and BookingNumber not in (select BookingNumber from tblBookingContent where BookingStatus=1)
group by SegmentId