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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