The color for each layer can be modified by selecting Layers from the View menu, which pops up the View/Edit Layers dialog, as shown below. Click on the buttons in the Edit column to change the colors. You can also change the visibility of layers in this dialog. If you want to use system colors, select this option, current colors will be used when opening any project.
If you updated the version from the site and you don’t like the default color scheme of the layers, then most likely there is a checkmark “Use system colors”. In order to change the color scheme it is not necessary to manually change the configuration file after you have updated the version from the site. Simply:
Now reading the color set will be from the file. Reopen your file (that was used before updating the version of Freepcb)