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This is NOT part of Akeeba CMS Update. The aforementioned SQL query is part of Joomla! itself. You will get the same message when updating using Joomla! Update or if you install the update directly.

Why do you get this message? For performance reasons Joomla! has decided to migrate all tables from the old MyISAM engine to the much more performant InnoDB engine. The SQL query you quoted does exactly that for the #__menu table. However, full text search search (FULLTEXT) indices are only supported on InnoDB tables since MySQL 5.6, see https://dev.mysql.com/doc/refman/5.6/en/innodb-fulltext-index.html

Here's the deal: the #__menu table, as shipped by Joomla! itself, DOES NOT have a fill text index. This is why the Joomla! project decided to safely move these tables to the InnoDB storage engine. Therefore a third party extension or someone with database access to your site has modified the core Joomla! tables. This is what is causing the problem and will prevent any future updates of Joomla!, as well as prohibit the smooth operation of your site.

Short-term solution: remove the FULLTEXT index from the xpqe_menu table, go to Extensions, Manage, Database and click on Fix.

Long-term solution: ask your host to update MySQL to version 5.6 or 5.7. This will give you at the very least another 3-4 years of trouble-free database experience.

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Hm, that's strange, because the actual message says that the menu table can't be converted. Is it possible that you have a FULLTEXT index in another table and for whatever reason Joomla! reports the wrong SQL query?