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This is not a dynamic property, which means it must be set when mysql server gets started. You need to add this into the my.cnf (or my.ini on windows) under the [mysqld] section:
What error did you get in your mysql log file? Not sure whether this is what the problem is but if your file is 400M and you attempt to limit the size to 40M then this could be a problem.
An associated parameter is innodb_data_home_dir:
The paths to individual data files and their sizes. The full directory path to each data file is formed by concatenating innodb_data_home_dir to each path specified here
This is normal as the header of the file will include some internal structures which are updated regularly. You can always increase the configuration of ibdata1 to be larger or start removing unwanted tables which are placed in this file which should free up some space. Or put back the autoextend parameter to allow it to continue growing without any checks.