Creating a branching scenario

I think this will depend quite a bit on your current code and the effect you are after

For instance if they are clicking an mc in flash then you could add this _alpha = 50 to the onclick function That dim the mc when it is clicked  

Hi James,

Currently I have:

tools onRelease = function() {
   _level0 ArtAPI PlaySlideNum(11);
};
docs onRelease = function() {
   _level0 ArtAPI PlaySlideNum(26);
};
tubes onRelease = function() {
 _level0 ArtAPI PlaySlideNum(37);
};
safety onRelease = function() {
 _level0 ArtAPI PlaySlideNum(31);
};
waste onRelease = function() {
 _level0 ArtAPI PlaySlideNum(34);
};
back onRelease = function() {
 _level0 ArtAPI PlaySlideNum(43);
};

I've even tried changing the state of the button once  hit in the Timeline but that didn't have any affect to the button once being redirected to this stage again

Try this When the button is clicked it will become 50% transparent Depending on what the button looks like and the background behind it this might work OK  

tools onRelease = function() {
   _level0 ArtAPI PlaySlideNum(11);

   this _alpha = 50;
};

I am unsure of what you are using for the button Another way to handle this would be two have an mc in the button that is a graphic of and X or strike-through or whatever This mc, we'll call it stike_mc, is set to normally not be visible Then when clicked do this:

tools onRelease = function() {
   _level0 ArtAPI PlaySlideNum(11);

   this strike_mc _visible = true;
};

Oh one thing we have not been considering is that when the user comes back to this slide it will be reloaded; wiping out all your settings  

You will want to set some _global vars or maybe use a Shared Object

James is there anyway to save this into the lms?

There is

There is but it is much more complicated!