Oracle 18c

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CREATE TABLE table_name (column1) AS
SELECT 'A~B~C~D~E~F' FROM DUAL;
1 rows affected

SELECT SUBSTR(column1, 1,      p1 - 1 ) || '~' ||
       SUBSTR(column1, p2 + 1, p3 - p2 - 1) || '~' ||
       SUBSTR(column1, p4 + 1, p5 - p4 - 1) AS column1_new
FROM   (
  SELECT column1,
         INSTR(column1, '~', 1, 1) AS p1,
         INSTR(column1, '~', 1, 2) AS p2,
         INSTR(column1, '~', 1, 3) AS p3,
         INSTR(column1, '~', 1, 4) AS p4,
         INSTR(column1, '~', 1, 5) AS p5
  FROM   table_name
)


COLUMN1_NEW


A~C~E


SELECT REGEXP_REPLACE(column1, '([^~]+)~[^~]+~([^~]+)~[^~]+~([^~]+).*', '\1~\2~\3' )
         AS column1_new
FROM   table_name;


COLUMN1_NEW


A~C~E