The safest course of action is to stop MySQL on both machines and copy the table files you need from the
mysql schema from slave to master, saving copies of the files. As long as they are MyISAM tables (not InnoDB), this is a legitimate operation.
If you can't shut down the machines, then connect to both of them and run
FLUSH TABLES WITH READ LOCK; wait for the prompt to return, and then leave the connections open (to hold the locks) while copying the files. Then
UNLOCK TABLES; to release the global read lock. MyISAM tables are pretty flexible this way... you need to copy the MYD and MYI files for the tables, together in pairs, and you should probably copy the matching .frm files on the off chance that they aren't identical (though they should be)... just save copies of anything you overwrite, and don't try this with InnoDB tables.
This should restore the procedures; you might need to restart the server for them to be recognized by all threads (but I don't think so).
If changes to tables in
mysql normally replicate in your setup, that tends to suggest underlying system trouble ... or someone else with access to the system not quite knowing with they are doing ... or a potential security breach, and, unfortunately, none of these things really jumps out to me as more likely than any other, though my instinct is to be "suspicious of malicious."
Since you do have binary logging enabled, you should review the binlogs from around the period of time the timestamps suggest using
mysqlbinlog --verbose --base64-output=decode-rows, since even though the slave didn't change its tables, that doesn't mean there couldn't be something interesting in the binlog that changed something else that you haven't yet discovered, or that did not have the same impact on the slave for any number of other reasons, like
I would check all of the grant table contents along with everything else in the
mysql schema. I would also reconfigure the servers with
log_warnings = 2, which logs access denied errors, and I might even be tempted to turn on the general query log for a while if your system has the I/O capacity to support that without performance penalty. I would further configure the local machine to forward a copy of its syslog messages to another system with tightly restricted access, and thoroughly audit the firewall... all of this is a little bit alarmist-sounding, but without some other evidence of filesystem problems, that certainly can't be considered the most likely thing to have happened.