ib_logfile0 differnce in size mysql 5.5.28 exception

[Venkatesh Ramanujam]

I am using mysql 5.5.28

got the below exception while starting mysql

180125 02:59:42 mysqld_safe Starting mysqld daemon with databases from /opt/custom/data/mysql/
180125 2:59:42 [Warning] /usr/sbin/mysqld: ignoring option '--character-set-client-handshake' due to invalid value 'utf8'
180125 2:59:43 [Note] Plugin 'FEDERATED' is disabled.
180125 2:59:43 InnoDB: The InnoDB memory heap is disabled
180125 2:59:43 InnoDB: Mutexes and rw_locks use GCC atomic builtins
180125 2:59:43 InnoDB: Compressed tables use zlib 1.2.3
180125 2:59:43 InnoDB: Using Linux native AIO
180125 2:59:43 InnoDB: Initializing buffer pool, size = 4.0G
180125 2:59:43 InnoDB: Completed initialization of buffer pool
InnoDB: Error: log file ./ib_logfile0 is of different size 0 4091904 bytes
InnoDB: than specified in the .cnf file 0 5242880 bytes!
180125 2:59:43 [ERROR] Plugin 'InnoDB' init function returned error.
180125 2:59:43 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
180125 2:59:43 [ERROR] Unknown/unsupported storage engine: InnoDB
180125 2:59:43 [ERROR] Aborting



When we started looking for the issue we found out that my.cnf was modified and there was a copy of MySql DB kept under /tmp folder and the same file was null in the actual mysql folder we copied the file from /tmp and tried to restart the DB when we got the error saying that the DB is corrupt

but when does my.cnf gets corrupted ? we haven't modified the my.cnf and no other application changes it. whenever mysql server crashes / when the mysql process gets killed by kill -9 does the my.cnf file configuration gets modified ?