Hi Everyone,
I have an explanation from the devs on how the color scheme works. First thing to understand, there is a special eaglerc flag that controls the behavior of the layer colors it is:
SET Layer_Colors_From_Settings OFF
It can be set to OFF or ON. If it is set to ON, then whatever colors are set in the eaglerc file (Fusion has one) will override whatever colors are stored in the schematic and board. If it is set to OFF then whatever colors are saved in the schematic and board prevail. So that's the first piece of the puzzle.
Second piece. What colors get saved to the eaglerc file? Let's say you have a schematic and board with layer 110(number is arbitrary just has to be above 100 which is where user defined layers believe). On the schematic layer 110 is red and on the board layer 110 is green. Whichever editor is closed last wins, so if you close the schematic and then the board green will be saved as the color for layer 110 in the eaglerc. If you reverse the order then layer 110 will be saved as red in the eaglerc. Normally not much of an issue since by default we avoid using the same layer numbers in the schematic and the board.
So @RitchieFromParis, here's what you could do.
Set the Layer colors from settings option to OFF. Make whatever changes in the layer colors you want to make and save the design. These are the colors you will always see when you open this design. New designs will use the built-in defaults.
If you want to always use certain layer colors then make sure the above setting is set to ON. Make whatever changes you want to the layer colors and then make sure that the last editor you close is the one you made the layer color changes to. So if you changed layer colors on the board, make sure you close the schematic before you close the board.
I know it's tricky but it's how it works right now. @silvio3105 as you can see colors are stored in the files but they can be overwritten by whatever is stored in the eaglerc config file.
Let me know if there's anything else I can do for you.
Best Regards,

Jorge Garcia
Product Support Specialist for Fusion 360 and EAGLE
Kudos are much appreciated if the information I have shared is helpful to you and/or others.
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