La tua richiesta
INSERT INTO custom_values
(Issue, issues.id, 4, versions.name)
SELECT * FROM issues INNER JOIN versions ON issues.fixed_version_id=versions.id;
dovrebbe essere modificato in questo
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;
per essere SQL valido.
Ma farei comunque il backup del db... :-)