Running this on MySQL 5 (Amazon RDS) on a large instance (i.e. very powerful), this query takes 16 seconds to execute. This InnoDB table has about 2 million rows.
DELETE FROM quiz_multichoice_user_answer_multi WHERE
user_answer_id IN( SELECT id FROM
quiz_multichoice_user_answers WHERE question_nid =
1001700 AND question_vid = 1002731 AND result_id =
64003
Rewrite it to use JOINs instead of a subquery and see if that improves things. It often does with MySQL; the query planner is better at optimizing joins, and choosing good indexes when they’re used, for whatever reason.