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https://issues.apache.org/jira/browse/CASSANDRA-3488?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Jonathan Ellis resolved CASSANDRA-3488.
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    Resolution: Cannot Reproduce

I remember you had some "dropping index didn't completely drop the index" 
problems with this cluster dating back to 0.7.x (which sounds like 
CASSANDRA-2619 to me, but there were a lot of index fixes in 0.7.5 and 0.7.6).  
That's probably the root cause.
                
> Secondary indexes still around 3 months after deleting them
> -----------------------------------------------------------
>
>                 Key: CASSANDRA-3488
>                 URL: https://issues.apache.org/jira/browse/CASSANDRA-3488
>             Project: Cassandra
>          Issue Type: Bug
>    Affects Versions: 0.8.4
>            Reporter: Jeremy Hanna
>              Labels: secondary_index
>
> We had an issue where we lost the data directories of two nodes.  So we 
> re-bootstrapped those two nodes into the cluster and did the repair.  During 
> the repair, secondary indexes were built as evidenced both in compactionstats 
> and in the filesystem.  The problem is, we haven't had secondary indexes on 
> any of our column families for about 3 months now.  The history there is that 
> we were on 0.7.6, deleted the secondary indexes on that version, and upgraded 
> to 0.8.4 a bit later.  It bootstrapped and repaired last night and this 
> morning, but it's been a good 10 hours today of almost exclusively rebuilding 
> secondary indexes that shouldn't be there.

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