I would say that once you have a file on the iPod and it works as expected then you can safely remove all copies of the file except the one that iTunes relies on directly, and copies that you intend to use further. For instance, you might want to watch HandBrake's output on your Mac or experiment with different quality/encoding settings in Podner. To determine which file iTunes relies on select a track in iTunes, then select Show Song File from the File menu.
_________________ Keith GugliottoPrimordial Sea CaptainSplasm Software https://www.splasm.com
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