Sorry, I don't understand, what needs to be updated there? The page explains how to install flixel, not flixel-tools.
If the flixel command does not work after you ran "haxelib run flixel-tools setup", something must've went wrong with copying the flixel.bat in the bin subdirectory of flixel-tools to "C:\HaxeToolkit\haxe" (that's the default location for haxe installations anyway, could be different for you). You can manually copy that file there and it should work.