How do I change the color of a few faces from the Brep.Faces array?

Brep entity drawing is optimized, so you need to recompile the entity after changing any face color. For version 2022:

myBrep.Faces[5].ARGB = Color.Red.ToArgb();

myBrep.RegenMode = regenType.CompileOnly;
myBrep.Compile(new CompileParams(design1));

design1.Invalidate();

For previous versions:

myBrep.Faces[5].Color = Color.Red;

myBrep.RegenMode = CompileOnly;
myBrep.Compile(new CompileParams(design1));

design1.Invalidate();