Symptoms

There is a common issue that can occur when customizing the color for the highlighting, or header color, or any other configuration in the "Basic Configuration UI 16" module
will revert to the out of the box colors upon refresh. 

Cause

The reason why this is happening is because the theme that is selected is not the system theme, this could be Blimey, Blimey-Blue, etc.
This is usually done through a Global User Preference for a theme which can be seen here:

https://[INSTANCE].service-now.com/sys_user_preference_list.do?sysparm_query=nameLIKEtheme%5Esystem%3Dtrue

Resolution 

This is happening because there is a better way to make a customized theme.
Please follow this Link for the Docs: Create or customize a theme