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https://issues.apache.org/jira/browse/FLINK-20427?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17286453#comment-17286453
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Till Rohrmann commented on FLINK-20427:
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[~rex-remind], the sources are not affected by this problem. You have problems 
if you require your Flink job to have exactly once processing guarantees wrt to 
your sink or external systems you are interacting. If your setup tolerates 
duplicates in ES, then this is not a problem.

> Remove CheckpointConfig.setPreferCheckpointForRecovery because it can lead to 
> data loss
> ---------------------------------------------------------------------------------------
>
>                 Key: FLINK-20427
>                 URL: https://issues.apache.org/jira/browse/FLINK-20427
>             Project: Flink
>          Issue Type: Bug
>          Components: API / DataStream, Runtime / Checkpointing
>    Affects Versions: 1.12.0
>            Reporter: Till Rohrmann
>            Priority: Critical
>             Fix For: 1.13.0
>
>
> The {{CheckpointConfig.setPreferCheckpointForRecovery}} allows to configure 
> whether Flink prefers checkpoints for recovery if the 
> {{CompletedCheckpointStore}} contains savepoints and checkpoints. This is 
> problematic because due to this feature, Flink might prefer older checkpoints 
> over newer savepoints for recovery. Since some components expect that the 
> always the latest checkpoint/savepoint is used (e.g. the 
> {{SourceCoordinator}}), it breaks assumptions and can lead to 
> {{SourceSplits}} which are not read. This effectively means that the system 
> loses data. Similarly, this behaviour can cause that exactly once sinks might 
> output results multiple times which violates the processing guarantees. 
> Hence, I believe that we should remove this setting because it changes 
> Flink's behaviour in some very significant way potentially w/o the user 
> noticing.



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