Do you have good xperience with SoX ?
Greetinx MrFritzle
To convert a two channel "hi res" file to 16-bit 44100 flac I use a script that automates something like
sox --no-clobber -G INFILE.flac -b 16 OUTFILE.flac rate -v 44100 dither -s
--no-clobber means sox will not overwrite the original file, so choose a suitable name for OUTFILE.flac. Metadata will be preserved.
-G prevents clipping (otherwise happens often with this kind of conversion)
rate -v selects the best quality sample rate converter.
dither -s will use dithering and noise shaping to help preserve dynamic range and is recommended when downsampling. SoX manual always uses 'dither -s' in examples for this kind of conversion so I imitate like a monkey.
I've never been able to hear the difference between the hi-res originals and my conversions but I don't have the kind of DAC or amazing amp and speakers or suitable listening room or even a quiet environment that would allow any difference to be heard if it existed. The main thing is that it's 100% guaranteed that you won't find any deficiency on iPod and headphones.