MySQL 8.0

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CREATE TABLE table1 (
  `user` INTEGER,
  `line_number` INTEGER,
  `header` INTEGER,
  `Indexi` INTEGER
);

INSERT INTO table1
  (`user`, `line_number`, `header`, `Indexi`)
VALUES
  ('290045', '0', '0', '3122411'),
  ('290045', '1', '0', '3122411'),
  ('290045', '2', '0', '833'),
  ('8733', '0', '0', '66');
UPDATE table1 t1 INNER JOIN (SELECT `Indexi`,`user`, COUNT(*) cnt1 FROM table1 GROUP BY `Indexi`,`user`) t2
USING (`Indexi`,`user`)
SET indexi = 500
WHERE user = 290045 AND Indexi = 3122411 and cnt1 = 1
SELECT * FROM table1


user
line_number
header
Indexi


290045
0
0
3122411

290045
1
0
3122411

290045
2
0
833

8733
0
0
66