Update : I've been converting some 16/44 tracks to 24/88 using the Audiofile Sample Manager with very pleasing results.

Using XLD I first convert from FLAC to AIFF (as opposed to WAV) as this retains the metadata. Thankfully the Sample Manager can output in FLAC post conversion.

It's quite a slow process but worth the wait. It's the best I've heard on my system so far...