ToolBook has standard palette with 96 colors. You can not change 32 colors shown at the top of palette window.
But other 64 colors can be modified. 
For example you work with one palette and want your application work good in 256 color mode.(May be you have book palette or all bitmaps in your book have one palette).
If solidColors of book is true then your palette must have 256-96=160 colors. 
You can set solidColors of book to false and then you have 256-32=224 colors for your palette. 
But then you loose 64 colors from standard palette because when those colors are not solid they are useless in 256 color mode.
We can propose another way:

1. Set solidColors of book to true
2. Clear customColors of book:
step i from 1 to textLineCount(customColors of this book)
        textLine i of customColors of this book = "0,0,0"
end step

Now all colors are black.

3. Then you can edit some colors and make any colors you need.
Take these colors from your book palette.
In most cases you don't need many additional colors (5 or 10 colors is enough).

Now if your book palette include 32+x colors from ToolBook palette then color shift does not happen.