Difference between SET autocommit=1 and START TRANSACTION in mysql (Have I missed something?)

Being aware of the transaction (autocommit, explicit and implicit) handling for your database can save you from having to restore data from a backup.

Transactions control data manipulation statement(s) to ensure they are atomic. Being "atomic" means the transaction either occurs, or it does not. The only way to signal the completion of the transaction to database is by using either a COMMIT or ROLLBACK statement (per ANSI-92, which sadly did not include syntax for creating/beginning a transaction so it is vendor specific). COMMIT applies the changes (if any) made within the transaction. ROLLBACK disregards whatever actions took place within the transaction - highly desirable when an UPDATE/DELETE statement does something unintended.

Typically individual DML (Insert, Update, Delete) statements are performed in an autocommit transaction - they are committed as soon as the statement successfully completes. Which means there's no opportunity to roll back the database to the state prior to the statement having been run in cases like yours. When something goes wrong, the only restoration option available is to reconstruct the data from a backup (providing one exists). In MySQL, autocommit is on by default for InnoDB - MyISAM doesn't support transactions. It can be disabled by using:

SET autocommit = 0

An explicit transaction is when statement(s) are wrapped within an explicitly defined transaction code block - for MySQL, that's START TRANSACTION. It also requires an explicitly made COMMIT or ROLLBACK statement at the end of the transaction. Nested transactions is beyond the scope of this topic.

Implicit transactions are slightly different from explicit ones. Implicit transactions do not require explicity defining a transaction. However, like explicit transactions they require a COMMIT or ROLLBACK statement to be supplied.

Conclusion

Explicit transactions are the most ideal solution - they require a statement, COMMIT or ROLLBACK, to finalize the transaction, and what is happening is clearly stated for others to read should there be a need. Implicit transactions are OK if working with the database interactively, but COMMIT statements should only be specified once results have been tested & thoroughly determined to be valid.

That means you should use:

SET autocommit = 0;

START TRANSACTION;
  UPDATE ...;

...and only use COMMIT; when the results are correct.

That said, UPDATE and DELETE statements typically only return the number of rows affected, not specific details. Convert such statements into SELECT statements & review the results to ensure correctness prior to attempting the UPDATE/DELETE statement.

Addendum

DDL (Data Definition Language) statements are automatically committed - they do not require a COMMIT statement. IE: Table, index, stored procedure, database, and view creation or alteration statements.

In InnoDB you have START TRANSACTION;, which in this engine is the officialy recommended way to do transactions, instead of SET AUTOCOMMIT = 0; (don't use SET AUTOCOMMIT = 0; for transactions in InnoDB unless it is for optimizing read only transactions). Commit with COMMIT;.

You might want to use SET AUTOCOMMIT = 0; in InnoDB for testing purposes, and not precisely for transactions.

In MyISAM you do not have START TRANSACTION;. In this engine, use SET AUTOCOMMIT = 0; for transactions. Commit with COMMIT; or SET AUTOCOMMIT = 1; (Difference explained in MyISAM example commentary below). You can do transactions this way in InnoDB too.

Source: http://dev.mysql.com/doc/refman/5.6/en/glossary.html#glos_autocommit

Examples of general use transactions:

/* InnoDB */
START TRANSACTION;

INSERT INTO table_name (table_field) VALUES ('foo');
INSERT INTO table_name (table_field) VALUES ('bar');

COMMIT; /* SET AUTOCOMMIT = 1 might not set AUTOCOMMIT to its previous state */

/* MyISAM */
SET AUTOCOMMIT = 0;

INSERT INTO table_name (table_field) VALUES ('foo');
INSERT INTO table_name (table_field) VALUES ('bar');

SET AUTOCOMMIT = 1; /* COMMIT statement instead would not restore AUTOCOMMIT to 1 */

https://dev.mysql.com/doc/refman/8.0/en/lock-tables.html

The correct way to use LOCK TABLES and UNLOCK TABLES with transactional tables, such as InnoDB tables, is to begin a transaction with SET autocommit = 0 (not START TRANSACTION) followed by LOCK TABLES, and to not call UNLOCK TABLES until you commit the transaction explicitly. For example, if you need to write to table t1 and read from table t2, you can do this:

SET autocommit=0;
LOCK TABLES t1 WRITE, t2 READ, ...;... do something with tables t1 and t2 here ...
COMMIT;
UNLOCK TABLES;