Sounds like you need to MIFwash all of this stuff.
Designate one file to be the color reference.
Define all used colors as desired.
Import to all other files.
Delete unused colors in all files (if you can't delete them, they aren't unused).
"Don't print" in color Defs should be unnecessary.
Use Color Views to switch author/review-only colors on and off.
The "inconsistent" can be as trivial as Spot vs. Process.
These are not "error" messages, rather FM's way of syaing that you have different settings for the colours applied in different chpaters - hence, inconsistent. It really won't affect your output either, unless you actually have content in some of those colours and perhaps set to not print - then they will disappear from thee relevant chapter.
If you've set some colours to "Do not print" in some chapters, but not in others, then this is the likely cause of the message. There is no advantage to this setting unless you are painstakingly trying to create individual Spot colour plates for some arcane woorkflow from the last century...
If you want to have some colours that contain content that you do not want to output, then a don't print setting will also be useful. I tend to prefer to use the Color Views and set some custom colours to "Invisible" in View 1 (the default) and have them show in View 6. This way I can quickly toggle on/off (esc v 6 - switches to view 6; esc v 1 - switches back to view 1) guide lines, background grids, comment frames (text frames with processing instructions or some form of comment) - works much like a "layer" in Illustrator or Photoshop, except it is based solely on colour attributes, not objects themselves.