MySQL binlog missing queries
That is true in the context of binlog-do-db (and equivalent) using STATEMENT based replication. You should never use binlog-do-db unless you know what you are doing (or you will lose data because of replication filters). If you want to do replication filtering, you should use replicate-wild-do-table (and other wild options) on the replica. It is easy to filter out events, but impossible to put them back if they were never logged. ROW sometimes can also help saner filtering behaviour.

If you are not using replication filtering, all write commands that are not server specific are sent to the master's binlog, if enabled correctly and not truncated/expired.

You need to provide more information to understand the issue you suffered (mysql version, topology used and options).