Replication Issue - Changing the replication-do-db filter
If I understand correctly: You have two DB's in a Master &lt;-> Master setup, but one of them has the replicate-do-db rules meaning they are now (potentially) out of sync?

At present the DB with the replicate-do-db options is only replicating (processing) statements where the database concerned is in the list (the precise rules vary depending on whether you are using Statement Based or Row Based Replication).

http://dev.mysql.com/doc/refman/5.1/en/replication-options-slave.html#option_mysqld_replicate-do-db

Unfortunately the CHANGE REPLICATION FILTER option has only just been introduced in MySQL 5.7, prior to that you will need to find the set of entries in the my.cnf file for your database with the replicate_do_db = statements. 

You will need to remove / hash (#) these out, and then restart MySQL.

After that the DB will replicate all statements that are passed across from the other master. 

The final thing you will probably want to do is run something like pt-table-checksum to check the consistency of the two DB's. If needs be you may need to dump/recreate the second DB to make it consistent with the first one.