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Well in your case its not Geany, its Java. My guess is java decides what the file encoding is from the environment it inherits from Geany when Geany runs the build command, which is the environment Geany inherited when it was started by the wrapper, which is what was set in the conf file.
There is no other way of passing the information of what the file encoding is to Java AFAIK (unless there is a command line option you can add), so the encoding of the file that Geany edits is not visible to Java.
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