Come controllare la data minima in ogni osservazione e aggiornare il flag in modo dinamico

Poiché questa è la domanda originale, sto postando la risposta qui. Suggerirei di abbandonare i tuoi loop tutti insieme. Ecco un modo con 2 CTE e ZERO loop.

declare @table table (ID int, StartDate date, EndDate date)
Insert Into @table
(
    ID
    , StartDate
    , EndDate
)
Values
(1,     '2017-01-01',    '2017-02-01'),
(1,     '2017-01-09',    '2017-01-28'),
(1,     '2017-04-01',    '2017-04-30'),
(1,     '2017-04-05',    '2017-05-20'),
(1,     '2017-04-20',    '2017-06-12'),
(2,     '2017-06-02',    '2017-06-20'),
(2,     '2017-06-14',    '2017-07-31'),
(2,     '2017-06-14',    '2017-07-31'),
(2,     '2017-06-19',    '2017-07-31'),
(2,     '2017-06-19',    '2017-07-31')


;with cte as(
select
    t1.ID
    ,t1.StartDate
    ,t1.EndDate
    ,DT = (select min(StartDate) from @table t2  where t2.StartDate > DATEADD(day,30,t1.StartDate))
from
    @table t1),

cte2 as(
select
    ID
    ,StartDate
    ,EndDate
    ,dense_rank() over (order by isnull(DT,(select max(StartDate) from cte))) as Flag
from
    cte)

select 
    ID
    ,StartDate
    ,EndDate
    ,case when Flag % 2 = 0 then 2 else Flag % 2 end as Flag
from cte2