Does MySQL foreign_key_checks affect the entire database?

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It is session-based, when set the way you did in your question.

https://dev.mysql.com/doc/refman/5.7/en/server-system-variables.html

According to this, FOREIGN_KEY_CHECKS is “Both” for scope. This means it can be set for session:

SET FOREIGN_KEY_CHECKS=0;

or globally:

SET GLOBAL FOREIGN_KEY_CHECKS=0;

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