Cool Color Changes Gary
The Color Replacer Tool will change ALL colors that are "near" the same color so many colors that you do not want to change will also change.
a way to get around this is to start by replacing all Civ Colors, smoke and shadows on the Palette with Magenta. You will only have the Unit Colors then.
You can use the Color Replacer Tool to change colors to the unit without changing Civ Colors, Smoke or Shadow shades. Use this for adding the new colors to the Original Palette. Make the Palette Color Changes with Pedit and save the new Palette. Note that you Keep all of the Unit Color slots in the same positions on the New Palette so all will keep the same Index. You just Copy over the Changed Unit Colors to each Original Slot.
You will need to make a separate Storyboard with ONLY the Smoke and Shadow Colors for the Unit Flc.
Change the Frame Lines to Black or some other Pure Color.
To do this, Load a Palette that has ONLY all Smoke and Shadow shades on it to the Original Storyboard. This Palette has all other Slots in the palette colored Black for example. Apply this palette Using Maintain Indexes. All Unit colors will then be Black other than Smoke and Shadow shades. Change the Frame Lines to another Color with Flood Fill. You can start by Changing the Frame Lines to a Medium Shadow or Smoke Shade that you can see.
Use the Color Replacer Tool to change the Black color to Magenta and you will have Just the Smoke and Shadow Shades for that Storyboard. Flood Fill the Frame Lines with Black again so you can see them better for Copy/Paste Procedure.
Apply the New Color Palette to your Unit Storyboard.
Change the Smoke and Shadow shades on this storyboard to Pure Colors so each is a different Pure Color. Do the same change to all smoke and shadow shades on the Smoke and Shadow Storyboard you made. Each Shade on both storyboards should have the exact Same Color, no matter what color you use for them. Use Colors that are Not found in the Unit Palette for that Unit...When I say Pure Colors, I mean the Pure Colors found on the little Palette you will see when you edit the palette (Shift+P) and double left click a color pixel on the unit palette. Those Colors are all usable pure colors for this purpose.
Now both have the same pure colors for each smoke and shadow shade. Looks Weird I know...no problem.
This allows you to Copy and paste the Smoke and Shadow areas to the Storyboard you changed the Unit Colors for without them matching the wrong subtle smoke or shadow shade.
I usually Flood Fill the Frame Lines with Black so I can see them Clearly on Both Storyboards. This is what is Used for Copy and Paste procedures...the Frame Lines.
Make sure you place the Background Color (Magenta) in the "Background and Fill Properties" Box so the Background will not copy or paste...only the Frame Lines and Other Colors from your Smoke and Shadow storyboard will.
Using the Rectangle selection Tool, you can Copy (Ctrl+C) 4, 5 or 6 Frames across and 4 Frames Down then Paste them as a "Floating" Image (Ctrl+Shift+E) that you can Move around on the New storyboard. Line up the Frame Lines exactly and set the image (Left Click) and final set (Right Click).
Use a Size for your Storyboards you can see ok to copy and paste....usually 100 will do if you can see the Frame lines exactly. You do not have to Copy the entire Frame Lines...just enough that will allow you to place the Image accurately when you paste. Corners and or Some Vertical and Horixontal Frame lines will do it.
After Completing the Copy and Past procedure to place the Smoke and Shadows to your New Storyboard, Simply Load your New Palette and Maintain Indexes to make all smoke and shadow shades correct.
Note...Yes the Smoke and Shadow shades will look totally Weird with all the Pure Colors you changed them to for Copy Paste reasons but this will make sure all shades maintain the same shades they are suppose to be when finished. IF you try to copy/paste without changing those shadow and smoke shades to a pure color...some will not paste correctly. The Lighter Shades of magenta that are used will paste as pure magenta or another incorrect shadow or smoke shade because all are too much the same for the Program to differentiate.
IF you just want to, you can either Remove all Frame Lines on the Finished Storyboard or Change them to the #254 Color on your Palette. Flicster will add the Frame Lines and use #254 color when you generate the New Flc from the storyboard regardless.
Hope this makes some sense

It is Naturally Faster than anyone can read this

Gary...if any questions, just send me a PM or E-Mail.