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When MySQL refuses to use your index, there's a number of things that you may be doing wrong. One of them might be conditions with improper data types.

...assume you have a users table with an email field (varchar) which is indexed. MySQL will use the index when your query is well-formed: mysql> EXPLAIN SELECT * FROM users...

If replication is broken by a simple invalid query, i.e. grants change, etc. you can force-skip that query: