How to recover performance_schema after restoring from partial innobackupex backup?
The solution requires running mysql_upgrade on the server that has been restored. As per the documentation on https://dev.mysql.com/doc/refman/5.5/en/performance-schema-build-configuration.html


  If you install MySQL over a previous installation that was configured without the Performance Schema (or with an older version of the Performance Schema that may not have all the current tables), run mysql_upgrade after starting the server to ensure that the performance_schema database exists with all current tables. Then restart the server.