i had the same issue 2 months ago, there are two different ways to use BrawlEX, and in one of the way's, you replace the CSS file and two common files, this way, is not campatible with the Custom CSS code, deleting all the characters, look, here is a tutorial of how to use the EX Engine compatible with the code:
https://www.youtube.com/watch?v=UoWad-wuqFs