Problem Re-indexing AFTER ES Upgrade 2.x to 5.x

Hi There ES Community,

I upgraded my ES Cluster from 2.x to 5.x. However, in the midst of a busy morning I forgot to run the migration tools. The upgrade went smoothly, re-configured my ES and launched it only to find it failing.

Looking through the logs the following message caught my attention:
java.lang.IllegalStateException: The index [kibana-int] was created with version [0.90.9] but the minimum compatible version is [2.0.0-beta]. It should be re-indexed in Elasticsearch 2.x before upgrading to 5.5.1

Now this would be all good and dandy if I had NOT upgrade my Cluster. Is there any way to re-index this particular Index (This seems to be the only one incompatible) without having ES running? I have to re-index this particular index with ES but cannot launch ES to re-index.

I am willing to delete this index as well but I cannot do this without running through ES API, can I? Perhaps just delete a particular folder and it magically deletes the index and ES launches? Any help or workout is appreciated?

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