SQLite 3.27

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CREATE TABLE mytable(
   id        INTEGER  NOT NULL PRIMARY KEY 
  ,timestamp VARCHAR(28) NOT NULL
);

INSERT INTO mytable(id,timestamp) VALUES (1,'2020-09-06 15:08:21.128344');
INSERT INTO mytable(id,timestamp) VALUES (2,'2020-09-06 15:08:21.128344');
INSERT INTO mytable(id,timestamp) VALUES (3,'2020-09-06 15:08:21.128344');
INSERT INTO mytable(id,timestamp) VALUES (4,'2020-09-06 15:08:22.128344');
select t.*,
	substr(timestamp, 1, 20) || (
		1000 * (row_number() over(partition by timestamp) - 1) 
		/ (count(*) over(partition by timestamp))
	) new_timestamp
from mytable t


id
timestamp
new_timestamp


1
2020-09-06 15:08:21.128344
2020-09-06 15:08:21.0

2
2020-09-06 15:08:21.128344
2020-09-06 15:08:21.333

3
2020-09-06 15:08:21.128344
2020-09-06 15:08:21.666

4
2020-09-06 15:08:22.128344
2020-09-06 15:08:22.0


select t.*,
    substr(timestamp, 1, 20) || (
        1000 * (row_number() over(partition by datetime(timestamp) order by id) - 1) 
        / (count(*) over(partition by datetime(timestamp)))
    ) new_timestamp
from mytable t


id
timestamp
new_timestamp


1
2020-09-06 15:08:21.128344
2020-09-06 15:08:21.0

2
2020-09-06 15:08:21.128344
2020-09-06 15:08:21.333

3
2020-09-06 15:08:21.128344
2020-09-06 15:08:21.666

4
2020-09-06 15:08:22.128344
2020-09-06 15:08:22.0

id	timestamp	new_timestamp
1	2020-09-06 15:08:21.128344	2020-09-06 15:08:21.0
2	2020-09-06 15:08:21.128344	2020-09-06 15:08:21.333
3	2020-09-06 15:08:21.128344	2020-09-06 15:08:21.666
4	2020-09-06 15:08:22.128344	2020-09-06 15:08:22.0