How to replace a font in /System/Library/Fonts/Supplemental/ with a newer version?

You can't replace system fonts, but you can put the newer one in Library/Fonts or Home/Library/Fonts. Making sure the app uses the right one may depend on the app. Which app are you mainly using for your Brahmi work?

Since Big Sur, the System folder and everything in it is completely untouchable. You cannot remove, or add anything to that folder or its subfolders. And beginning with Ventura, you can no longer disable even the mostly useless fonts in the Supplemental folder (I still don't understand that one).

You can try adding your updated font, but if the internal names are the same, this will create a font conflict. Then what happens is a bit random. A given app may continue to list the System installed font. It may show the one you added. Most times, the app will show neither since it can't know which one you're trying to use.

When you place the newer Brahmi font per Tom Gewecke's recommendation, you may contribute to a named duplicate font scenario and the operating system may resolve it by using the System Brahmi version, not the one you add. This is because the System ordered search for Fonts is:

1. /System/Library/Fonts
   1. ../Supplemental
2. /Library/Fonts
3. /Users/username/Library/Fonts.