This is strange. We have been building a new Moodle site for the last few months and had been running on 3.5.2. I have a custom theme I've developed with its own settings which has been working great. After upgrading to 3.5.3 yesterday none of my theme settings are maintained after I click save. If I enter a value into a theme setting textbox for example and hit save its simply empty after the page refresh.
I'm still pretty new to Moodle and am not able to parse the complete contents of the upgrade on my own to understand how this could happen.
My theme uses Boost as a base theme.