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I did this with my library (actually I went from .wav to apple lossless) - but I just used iTunes. You can add the field "kind" to the table and sort the files that way, deleting the originals after the copies are made. Just make sure that you've doubled the number of items in your library before you delete! I don't think there would be a good way of doing this without using iTunes. After all, the program would need to alter the itunes xml and library files or else all of your music will be missing from your library! Given what a pain in the ass that would be, I preferred to manually delete things after conversion.
Of course, this method, while relatively safe, requires that you have a bit of extra storage and, depending on the size of your collection, a bit of time. I did my library (8,000 tracks of mostly classical music, so approx. 32 days worth of music originally stored in 400 gb) is a couple of days. It went surprisingly well.
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Cogito ergo spud -- I think, therefore I yam
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