So I did more digging into scale modes and such and figured out a solution.
I created a CustomScaleMode that extends FixedScaleMode and overrode the onMeasure function:
override public function onMeasure(Width:Int, Height:Int):Void {
FlxG.width = Width;
FlxG.height = Height;
updateGameSize(Width, Height);
updateDeviceSize(Width, Height);
updateScaleOffset();
updateGamePosition();
}
Using this CustomScaleMode I was able to simply restart the state (ex. FlxG.switchState()) and the game was rendering at the new resolution.
So far it works well, I hope this helps others with the same problem.
EDIT: I also just realized that FlxG.resetGame() exists.
