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https://issues.apache.org/jira/browse/CASSANDRA-13079?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15780296#comment-15780296
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Marcus Olsson commented on CASSANDRA-13079:
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How are you running repair? If repair is run without the '--full' flag I 
believe this is the expected behaviour due to incremental repair being default 
since version 2.2. Incremental repair basically doesn't repair the data that 
has previously been repaired, which could explain the above situation.

> Repair doesn't work after several replication factor changes
> ------------------------------------------------------------
>
>                 Key: CASSANDRA-13079
>                 URL: https://issues.apache.org/jira/browse/CASSANDRA-13079
>             Project: Cassandra
>          Issue Type: Bug
>          Components: Core
>         Environment: Debian 
>            Reporter: Vladimir Yudovin
>            Priority: Critical
>
> Scenario:
> Start two nodes cluster.
> Create keyspace with rep.factor *one*:
> CREATE KEYSPACE rep WITH replication = {'class': 'SimpleStrategy', 
> 'replication_factor': 1};
> CREATE TABLE rep.data (str text PRIMARY KEY );
> INSERT INTO rep.data (str) VALUES ( 'qwerty');
> Run *nodetool flush* on all nodes. On one of them table files are created.
> Change replication factor to *two*:
> ALTER KEYSPACE rep WITH replication = {'class': 'SimpleStrategy', 
> 'replication_factor': 2};
> Run repair, then *nodetool flush* on all nodes. On all nodes table files are 
> created.
> Change replication factor to *one*:
> ALTER KEYSPACE rep WITH replication = {'class': 'SimpleStrategy', 
> 'replication_factor': 1};
> Then *nodetool cleanup*, only on initial node remained data files.
> Change replication factor to *two* again:
> ALTER KEYSPACE rep WITH replication = {'class': 'SimpleStrategy', 
> 'replication_factor': 2};
> Run repair, then *nodetool flush* on all nodes. No data files on second node 
> (though expected, as after first repair/flush).



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