This is based on the code for version 0.3.1, but 0.3.7 appears to also have the problem. Simple test to verify:

FLAC_FileEncoder encoder = new FLAC_FileEncoder();
File wavFile = new File("wav.wav");
File flacFile = new File("flac.flac");
encoder.encode(wavFile, flacFile);
wavFile.delete();

The last call fails, but it should succeed (assuming proper permissions, etc.).