To fix schema disagreements, you need to force the disagreeing nodes to rebuild their schema. Here's how:
Open the cassandra-cli and run: 'connect localhost/9160;', then 'describe cluster;'. You'll see something like this:
[default@unknown] describe cluster;
75eece10-bf48-11e0-0000-4d205df954a7: [192.168.1.9, 192.168.1.25]
Note which schemas are in the minority and mark down those IPs -- in the above example, 192.168.1.27. Login to each of those machines and cleaninly stop the Cassandra service/process, typically by running:
'sudo service cassandra stop' or 'kill <pid>'.
At the end of this process the commit log directory (/var/lib/cassandra/commitlog) should contain only a single small file.
Remove the Schema* and Migration* sstables inside of your system keyspace (/var/lib/cassandra/data/system, if you're using the defaults).
After starting Cassandra again, this node will notice the missing information and pull in the correct schema from one of the other nodes. In version 1.0.X and before the schema is applied one mutation at a time. While it is being applied the node may log messages, such as the one below, that a Column Family cannot be found. These messages can be ignored.
ERROR [MutationStage:1] 2012-05-18 16:23:15,664 RowMutationVerbHandler.java (line 61) Error in row mutation
org.apache.cassandra.db.UnknownColumnFamilyException: Couldn't find cfId=1012
To confirm everything is on the same schema, verify that 'describe cluster;' only returns one schema version.