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So after far too many hours of not managing to get a HD clip of a song into flipnote, I have finally created this tool that allows you to just choose your audio .wav file, your .ppm file, and it replaces the audio for you.
Doesn't seem like anyone other than me has asked for this but, well, if you ever need it its here now. Recording with the 3DS mic sounded BAD, I did want to try the method of recording pc audio straight into the mic input port with an aux splitter but uhh, the aux splitter just did nothing. But this works just fine instead.

https://github.com/Blurro/FlipnoteAudioReplacer/releases/
Have fun hopefully someone makes use of it
(i wasted so many hours fr)

Basic instructions:
  1. Get your .ppm file(s) from your SD card.
  2. Prepare your .wav file using Audacity to clip and convert however you need, up to 1 minute is Flipnote's limit.
  3. Drag and drop the .wav on the tool. The tool will spit out the compressed .adpcm file (basically just a headless wav, can be decoded using a sox command <-- that encode command does NOT work though)
  4. When prompted, enter your .ppm file extension included
  5. Put the newly created file back on your SD card (the filename is important but the tool sorts it for you)
If for some reason it doesn't work let me know, I usually do manage to leave in a silly oversight somewhere. Enjoy.