I think this jira is helpful for your question: 
https://issues.apache.org/jira/browse/FLINK-6328 
<https://issues.apache.org/jira/browse/FLINK-6328>

> Am 08.05.2017 um 19:33 schrieb Cliff Resnick <cre...@gmail.com>:
> 
> When a job cancel-with-savepoint finishes a successful Savepoint, the 
> preceding last successful Checkpoint is removed. Is this the intended 
> behavior? I thought that checkpoints and savepoints were separate entities 
> and, as such, savepoints should not infringe on checkpoints. This is actually 
> an issue for us because we have seen occurrences of false-positive successful 
> savepoints, perhaps due to S3 latency. Bottom line, we'd like to treat 
> savepoints as insurance rather than the critical path and would rather they 
> be oblivious to checkpoint management.
> 
> We are using externalized checkpoints, which may be confusing things. Also I 
> know checkpoint management is undergoing some changes in Flink 1.3 (we are on 
> Flink 1.2.0). Any insight is greatly appreciated.
> 
> 

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