First thing you should check is if binary logging is still enabled

mysql> SHOW BINARY LOGS; mysql> SHOW MASTER STATUS; 

These two commands will give you the list of binary logs it sees and the then the current binary log;

I cannot tell you how to delete the logs by database usage, but I can tell you three other ways:

1) DELETE ALL LOGS

The command to hose every binary log is

mysql> RESET MASTER; 

That's all.

2) DELETE LOGS BY BINLOG NAME

If you see 118 binary logs, you can select which log to delete up to. For example, if the binary logs have the form mysql-bin.000118, you can delete up to the 100th log using

mysql> PURGE BINARY LOGS TO 'mysql-bin.000100`'; 

3) DELETE LOGS BY DATE AND TIME

Suppose you want to delete all logs but keep everything from midnight 5 days ago. Run this:

PURGE BINARY LOGS BEFORE DATE(NOW()) + INTERVAL 0 SECOND - INTERVAL 5 DAY; 

or

PURGE BINARY LOGS BEFORE '2014-07-11 00:00:00'; 

This will let mysqld figure out which binary logs to delete.

GIVE IT A TRY !!!