Oracle 11g Release 2

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BANNER
Oracle Database 11g Express Edition Release 11.2.0.2.0 - 64bit Production
PL/SQL Release 11.2.0.2.0 - Production
CORE 11.2.0.2.0 Production
TNS for Linux: Version 11.2.0.2.0 - Production
NLSRTL Version 11.2.0.2.0 - Production

DECLARE
v_comment CLOB ;
v_comment2 CLOB ; 
v_sql CLOB;

BEGIN
--V_COMMENT := INCOMING_COMMENT || '[' || V_COMMENT || ']'; 
v_comment := 'process 456[process 123[process 123[process 456[process 000]]]]' ;

v_sql := q'{
with v_temp1 as (
  select '}'||v_comment||q'{' as comm0 from dual
  )
 , v_temp2 AS (
  select comm0
       , LEVEL lvl
       , regexp_count(comm0, '[^\[]+') cnt
       , trim(rtrim( regexp_substr(comm0, '[^\[]+', 1, LEVEL), ']' )) AS comm1
       , row_number()OVER(PARTITION BY comm0, trim(rtrim( regexp_substr(comm0, '[^\[]+', 1, LEVEL), ']' ))  ORDER BY LEVEL) rnb
  from v_temp1
  CONNECT BY LEVEL <= regexp_count(comm0, '[^\[]+')
 )
  SELECT listagg(comm1, '[') WITHIN GROUP (ORDER BY lvl) || 
         LPAD(']', regexp_count(listagg(comm1, '[')WITHIN GROUP (ORDER BY lvl), '\['), ']') comm2
  FROM v_temp2
  WHERE rnb = 1
}'
;

--dbms_output.put_line(v_sql); --test

execute immediate v_sql into v_comment2
;

dbms_output.put_line('input v_comment : ' ||v_comment ); --test
dbms_output.put_line('output v_comment2 : '||v_comment2); --test
END;
/

1 rows affected

dbms_output:
input v_comment : process 456[process 123[process 123[process 456[process 000]]]]
output v_comment2 : process 456[process 123[process 000]]