When editing a color in the color scheme (Tools -> Options -> LibreOffice -> Colors) by changing any of its values or picking a different color, the change only gets applied if one clicks the "modify" button afterwards. If one just makes changes and clicks "OK", the change does not get applied and there is no feedback.
This is not what I'd expect as a user, and it's quite frustrating if you (think that you) change a whole lot of colors, click "OK" and nothing is actually changed.
Admitted, the workflow is not user-friendly. Or rather _was_ because the way how palettes are handled is currently under review. Actually the area fill style dialog is completely revamped , and in course of this GSoC project the configuration page of tools > options > colors will be removed in favor of a user palette. You will be able to manipulate this (and only this) palette from the normal color section.
Modifying the factory settings of palettes will not be possible anymore. You need to hack the *.soc file directly , which is a piece of cake for experts (simple xml syntax).
The changes will be available in release 5.3. Thanks for filing the bug, although I close it as WONTFIX (feel free to reopen). It's always good to get expert opinions.
 <libreoffice>/share/palette/ (either at /opt or /usr)