IIRC the CON Tools might allow you to rreplace the audio file, but the new file needs to be in the correct MOGG format. You can’t just swap it with an mp3 ripped from your CD.
In addition, the new audio file must be perfectly aligned with the previous, otherwise the notes in the game will be out of sync. If the author has simply taken the audio from the CD, and you do the same, they should be aligned. But often the author decides to shift the audio forward in order to make room for the count-in.
If I were to replace a custom’s audio, I would extract everything with C3 Tools (use Phase Shift converter to downmix encrypted audio to stereo), open old audio and midi tracks in Reaper, add new audio there and make sure to align it correctly, encode/export the new audio from Reaper (also muted audio and fake dryvox – check correct formats from Farottone’s authoring tutorial), and rebuild in Magma.