Sua pergunta
INSERT INTO custom_values
(Issue, issues.id, 4, versions.name)
SELECT * FROM issues INNER JOIN versions ON issues.fixed_version_id=versions.id;
deve ser modificado para isso
INSERT INTO custom_values
(customized_type, customized_id, custom_field_id, value)
SELECT 'Issue', issues.id, 4, versions.name
FROM issues INNER JOIN versions ON issues.fixed_version_id=versions.id;
para ser SQL válido.
Mas eu faria backup do banco de dados de qualquer maneira ... :-)