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From what I understand you won't want to resample or change the bit depth of the original files themselves since this stuff can usually be done by BAE or the player.
That should be the case, but then why we must have to chose between 44100 or 48000 for input depending of what are we playing? If BAE does the proper conversion automatically, chosing the input sample rate would be redundant.
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Also I could be wrong but I believe it “converts 48000 to input 44100 and then converts back to 48000 for output”
I'm afraid it does so and according to my ears that extra step makes the audio suffer. I've found that a file converted to 44100 using HQ filters and dithering sounds way better than the orginal at 48000, but that's according me and I'm not really sure about it, that's why I'm asking what it really happens with BAE in this situation.