Sorry I haven't replied recently. School starting and what not. But actually he is using audacity; however, I have been able to determine that although it isn't perfect (cause truly, nothing is), it is good enough. The changes were too small for me to hear (like slight changes in pitch or volume), and probably not large enough for anyone but a trained ear to hear. Since my friend is the most talented musician I know, he could hear the slight changes and they really bothered him, but he made a version that he has called good enough. Really though, thank you for your offer! I appreciate all of your help and understanding! I'm so glad this is such a helpful community.
Thanks so much!
-Crynthus
Oh and also, RPG Maker VX Ace does not support .flac files, which I found here in case anyone else wants to know: http://www.rpgmakerweb.com/products/rpg-maker-vx-ace/material
and it's under "Formats available to Import"