If your slave does not also act as a master to another slave, then you should not have any issues from deleting binary logs. The relay logs are important to the slave.

You need to further investigate on why mysql schema disappeared. Is mysql schema still present on the disk, even though MySQL is not showing it? If you have not stopped the slave instance yet, then you could run under same user as MySQL is running:

lsof | grep '/path_to_mysql'

You might see mysql schema tables marked as deleted in there:

(deleted)

Another possibility is that you are connecting with a user that has limited privileges and just does not see mysql schema. Run SHOW GRANTS; to see what privileges you currently have.

As Rolando pointed out, use PURGE BINARY LOGS as best practice for cleaning up binary logs. If MySQL is down, you could delete the files manually, but then you have to also delete the same file names from the index file. Be careful on master servers, as binary logs might still be needed by slaves.

And if you do need to copy mysql schema, you can do it with just these steps on the slave. Although, I would recommend executing FLUSH TABLES; on master before doing these steps.

/etc/init.d/mysql stop
scp -rp master_server:/var/lib/mysql/mysql /var/lib/mysql/
/etc/init.d/mysql start

There is more stable approach you can try

Here is something to remember

Whenever you run CHANGE MASTER TO, it will erase every relay log you have. You do not want to keep relay logs of commands you have not executed any SQL on as of yet

The following is an excerpt taken from a post I made back on Feb 03, 2012 : How to resolve the master server shut down/unavailability in mysql with master - slave replication :

Please notice that there are two sets of replication coordinates from the Master

• (Master_Log_File,Read_Master_Log_Pos)
• (Relay_Master_Log_File,Exec_Master_Log_Pos)

There is a major difference between them

• (Master_Log_File,Read_Master_Log_Pos) tells you the last binlog statement from the Master's log file and log position that the Slave read from the Master and placed in its Relay Logs.
• (Relay_Master_Log_File,Exec_Master_Log_Pos) tells you the last binlog statement from the Master's log file and log position that the Slave read from the Master and placed in its Relay Logs THAT IS NEXT TO BE EXECUTED ON THE SLAVE.

What you want are two things:

1. Erase Every Binary Log You Have
2. Start Collecting Binary Log Entries From the Last SQL You Successfully Executed.

In your case, you must use the second set of Replication Coordinates

• Relay_Master_Log_File
• Exec_Master_Log_Pos

It is easy to distrust a corrupt relay log as shown in the error message. The one that hurts the most is a corrupt Master Log. You will have to jump through hoops if that is the case. On the other hand, if one of the other situations was the reason for the corrupt relay log, the simplest and most concise approach is what I stated.

To make sure, whatever is reported for Relay_Master_Log_File, if that particular binary log still exists on the Master, perform a mysqlbinlog on it. If it dumps in its entirety without corrupt characters, go ahead and use the second set of replication coordinates.

From my same earlier post

mysql> show slave status\G
*************************** 1. row ***************************
             Slave_IO_State: Waiting for master to send event
                Master_Host: 10.48.20.253
                Master_User: replicant
                Master_Port: 3306
              Connect_Retry: 60
            Master_Log_File: mysql-bin.000254
        Read_Master_Log_Pos: 858190247
             Relay_Log_File: relay-bin.066069
              Relay_Log_Pos: 873918
      Relay_Master_Log_File: mysql-bin.000254
           Slave_IO_Running: Yes
          Slave_SQL_Running: Yes
            Replicate_Do_DB:
        Replicate_Ignore_DB:
         Replicate_Do_Table:
     Replicate_Ignore_Table:
    Replicate_Wild_Do_Table:
Replicate_Wild_Ignore_Table:
                 Last_Errno: 0
                 Last_Error:
               Skip_Counter: 0
        Exec_Master_Log_Pos: 858190247
            Relay_Log_Space: 873772
            Until_Condition: None
             Until_Log_File:
              Until_Log_Pos: 0
         Master_SSL_Allowed: No
         Master_SSL_CA_File:
         Master_SSL_CA_Path:
            Master_SSL_Cert:
          Master_SSL_Cipher:
             Master_SSL_Key:
      Seconds_Behind_Master: 0
1 row in set (0.00 sec)

notice that the Replication Coordinates from SHOW SLAVE STATUS\G for what was last executed are (mysql-bin.000254,858190247). The CHANGE MASTER TO command in this case would be:

CHANGE MASTER TO master_log_file='mysql-bin.000254',master_log_pos=858190247;

Give it a Try !!!

UPDATE 2012-09-14 16:38 EDT

If you worried about the stockpiling relay logs, just throttle the relay logs. In SHOW SLAVE STATUS\G, there is a field called Relay_Log_Space. That gives you the sum of all relay sizes in bytes. Did you know you could put a cap on that number ?

The option is called relay_log_space_limit.

For example, if you want to cap the total number of bytes to 10G, do the following

STEP 01) Add this to /etc/my.cnf on the Slave

[mysqld]
relay_log_space_limit = 10G

STEP 02) Run service mysql restart on the Slave

and that's it !!!

When the oldest relay has all its entries processed, it is deleted and a new relay log is created. That gets filled until all relay logs add up to 10G. That's the only way to control runaway relay log space issues.

UPDATE 2012-09-14 18:10 EDT

SUGGESTION : If you make mysqldump backups of the data on the Slave every midnight, you could set up the following to restrict having 1TB of binary logs:

STEP 01) Add this to /etc/my.cnf on the Master

[mysqld]
expire_logs_days = 14

STEP 02) Run this query on the Master

mysql> PURGE BINARY LOGS BEFORE DATE(NOW()) - INTERVAL 14 DAY;

STEP 03) service mysql restart on the Master

STEP 04) Add a mysqldump backup script to a crontab on the Slave

This will make the Slave more useful and would control having excess binary logs to worry about