Per documentation, you should be using the refresh command after modifying an impala table in the way that you have described (modifying the HDFS directly). The refresh command has been documented in the following link: https://www.cloudera.com/documentation/enterprise/5-10-x/topics/impala_refresh.html You should execute a refresh command after removing the file from the HDFS. You do not need to execute the refresh command if you are adding a new partition in Impala, it is only needed if you are doing it via Hive or HDFS.
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