By definition, all Lossless Codecs will produce the same audio quality.
There may be slight filesize differences with varying Lossless Codecs.
If you are using iTunes and iDevices and see this continuing in the future, use ALAC for your Lossless audio Codec.
Just my opinion, given the assumptions I made.
If you have all (or most) of your current Lossy music in AAC format (not mp3) and are willing to use ALAC for your Lossless audio, you may use iTunes to re-rip your CDs into Lossless and 'replace' your Lossy (AAC) files, maintaining the current meta-data from the Lossy songs.
This works because both AAC and ALAC share the same file extension (.m4a). As long as the filename of the current Lossy song and the proposed Lossless version is exactly the same, iTunes will replace it with the better version maintaining the meta-data.
This will not work if you have an mp3 file that you want to morph into a ALAC file via iTunes.
This will not work if the song names and folder locations are not exact. i.e.:
a) The Eagles - This and That vs. The Eagles - This & That
b) The Eagles - This and That vs. Eagles - This and That
Even one character different will cause iTunes to create a separate file for that song.
While you may be able to 'spoof' iTunes by renaming all your mp3s so they have an extension of m4a, I do not know if this would work. I haven't tried it and may not have time for a test anytime soon.
Obviously, you do not want to lose your Lossy files during the 'replacement' process, so make several backups of them all to 2 or more ExternalHDs (if you havenlt already).
I am certain that this will be slightly to somewhat messy (or highly messy if bungled). Backups of everything is important.
This is what I would do if I found myself in your position. The meta-data management has to be well controlled so that your re-processing is kept to a minimum.
Still seems like less work than having to re-tag all your files.
There is most likely more important details that will come to me as I put more thought into this. Others may have additional suggestions or completely different approaches. Should be interesting to see the replies you get.
Best of Luck
4x Play:5 - 1x Connect:Amp - 1x Connect - 1x CR200 - 2x Bridge - QNAP TS-212 NAS w/12,000+ Apple Lossless Files - 2x HP Laptop w/Win7 Pro 64bit - Apple TV (2nd Gen) - AirPort Express - 2x iPhone 4S - 2x iPhone3G - iPod (3rd Gen)
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