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I do not believe that you can simply convert FLAC>Apple Lossless. I think you must convert from FLAC>Aiff (or Wav)>Apple Losseless.

FLAC support on the iPod would be great, but I think Apple Lossless more or less squashed the idea of FLAC support.
 
I generally find flac the best of the lossless compressions, but all are right, you will need to convert to uncompressed pcm files, (aiff/wav), then to apple lossless.

As a warning though, all lossless files are likely to drain your iPod's battery faster than you think it will. In theory, if your battery was 15 hours, because the file is 5 times the size, it could drain the battery in as little as 3 hours. More likely up to 5, but you get the picture.
 
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