Github user StefanRRichter commented on the issue: https://github.com/apache/flink/pull/3801 @gyfora this is already happening in the code: the backend tracks which files are already transferred to hdfs, and a reference counting in the checkpoint coordinator (introduced in FLINK-6014) takes care of deleting SSTable files from the shared HDFS directory that are no longer referenced by any incremental checkpoint.
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