You can drop the tables or truncate them ... but keep in mind that Cassandra will downsize your tables by default, so you will also need to run nodetool clearsnapshot on all of your nodes. There is no need to stop Cassandra while you delete it.
I do not know that there is a correct path as such ... but when I do it, when I need to clear the table, firstly, I run truncate in the table using cqlsh. Then I run nodetool clearsnapshot on my nodes using pssh ( https://code.google.com/p/parallel-ssh/ ).
Hope this helps
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