What happens to mysql information_schema after switching to innodb_file_per_table?
The information_schema database is an all memory database made up of temporary tables. It is not stored in any of the InnoDB plumbing.

I wrote about this 5 years ago : How is INFORMATION_SCHEMA implemented in MySQL?

If you performed a mysqldump of the infomration_schema, reimporting it will do nothing.

mysqld will correct and protect any outside manual attempts to change it.

For example, suppose you wanted to create a database called mynewdb and your datadir is /var/lib/mysql. if you ran the following commands

cd /var/lib/mysql
mkdir mynewdb
chown mysql:mysql mynewdb


This will create a database in the eyes of mysqld.

mynewdb shows up in INFORMATION_SCHEMA.SCHEMATA

You can verify this by running the following:

mysql&gt; SHOW DATABASES;
mysql&gt; SELECT * FROM information_schema.schemata;


The database mynewdb will be present

As for your actual question, don't worry. You cannot break the INFORMATION_SCHEMA. mysqld won't let you.