Trouble upgrading from 3.3.0 to 3.5.1

@Kjeld wrote:

In the table log_visit we have more that 52 million rows.
The update process is not finising while doing:

Executing ALTER TABLE `log_visit` MODIFY COLUMN `location_region` char(3) DEFAULT NULL;...
    [X] Error during plugin updates:

    * /var/www/piwik-3.5.1/core/Columns/Updater.php:
Error trying to execute the migration 'ALTER TABLE `log_visit` MODIFY COLUMN `location_region` char(3) DEFAULT NULL;'.
The error was: SQLSTATE[40001]: Serialization failure: 1213 Deadlock found when trying to get lock; try restarting transaction
    The update completed successfuly, however there were issues during the process. Please read the above descriptions for details. For further help:

Any suggestions on how to handle this?
I have maintenance mode enabled and loggin disabled.

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