_RefSkill, those IDs of your Lv125 skills are NOT properly matching with their respective chaining skills. E.g.
Code:
BEGIN
SELECT @ Basic_ChainCode = ID FROM _RefSkill WHERE Basic_Code = 'SKILL_CH_BOW_CHAIN_F2_01'
UPDATE _RefSkill
SET Basic_ChainCode = @ Basic_Chaincode
WHERE Basic_Code = 'SKILL_CH_BOW_CHAIN_F_01'
END
If you understand that simple query, you will figure out what's actually mismatching and causing your overlapping.
Another little hint: Not only the [ID] has to be adjusted before adding those skills to your database.
