Github user EronWright commented on the issue:
https://github.com/apache/flink/pull/3356
Would you mind having a look at `GlobalConfiguration.dynamicProperties`,
which is set by the main method of various Flink processes based on CLI
arguments. The `GlobalConfiguration.loadConfiguration` method (which loads
the YAML config) treats the dynamic properties as overrides to the config
entries. This feature is necessary because `loadConfiguration` is used all
over the place.
Just bringing it to your attention in case there's some interplay.
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