So I was working on retexturing this hack. http://forums.kc-mm.com/Gallery/BrawlView.php?Number=31346

I noticed that this model does not have any shading, so I exported the model to 3ds max and then retextured it there. This is where the textures (CMPR format in Brawlbox) that had transparency started showing no transparency in 3ds max. (Black instead of transparent).

After exporting it back to to Brawlbox and replacing the model, this fixed the shading problem. Unfortunately, I loaded it up in Brawl and the textures that used to be transparent were no longer transparent. (Just like in 3ds max).

So my question is: How do I get previously transparent textures to become transparent again?

EDIT: I solved the issue (after a few tries) using ramonM64's transparency guide!