Váš dotaz
INSERT INTO custom_values
(Issue, issues.id, 4, versions.name)
SELECT * FROM issues INNER JOIN versions ON issues.fixed_version_id=versions.id;
by měl být upraven na toto
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;
aby byl platný SQL.
Ale stejně bych zálohoval db... :-)