If your locale does not use "." for the decimal point, there is a bug that causes the default compression settings to be sub-optimal. You should add <spanclass="argument">-A "tukey(0,5)"</span> to your <spanclass="command">flac</span> command string (or however "0.5" should be formatted for your locale).
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If a corrupted FLAC file is used as input in FLAC-to-FLAC encoding, the transcoded FLAC file will have the audio data truncated after the first error.
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When encoding to Ogg FLAC, if there are too many seek points (>240), the seek table will not have the offsets written back properly after encoding.