SQLite 3.27

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CREATE TABLE tablename (
  `id` INTEGER,
  `timestamp` TEXT
);
INSERT INTO tablename
  (`id`, `timestamp`)
VALUES
  ('1', '2020-09-06 15:08:21.128344'),
  ('2', '2020-09-06 15:08:21.128344'),
  ('3', '2020-09-06 15:08:21.128344'),
  ('4', '2020-09-06 15:08:22.128344');
WITH cte AS (
  SELECT *,
    ROW_NUMBER() OVER (PARTITION BY timestamp ORDER BY ID) rn,
    COUNT(*) OVER (PARTITION BY timestamp) counter
  FROM tablename  
)
SELECT id,
       DATETIME(timestamp) || '.' || 
       SUBSTR('00' || ((rn - 1) * (100 / counter)), -2) timestamp
FROM cte       


id
timestamp


1
2020-09-06 15:08:21.00

2
2020-09-06 15:08:21.33

3
2020-09-06 15:08:21.66

4
2020-09-06 15:08:22.00

id	timestamp
1	2020-09-06 15:08:21.00
2	2020-09-06 15:08:21.33
3	2020-09-06 15:08:21.66
4	2020-09-06 15:08:22.00