Hey Jonatan,
Have you tried editing the project.xml or the include.xml? I am pretty sure that the include.xml has the higher priority when compiling for Windows, as stated in
this GitHub issue. Your include.xml is located in your "flixel" folder. I have mine in C:\app\sdks\haxe\3.0.0\haxe\lib\flixel\git, so I would edit that include.xml in the flixel\git folder. I think you only need to edit the include.xml of the library version you use, and I use flixel git in my projects, so I would edit only that one (not entirely sure if I edit just that one, or if I should edit all of them, so I may be wrong.)