We found the solution. Seams Android prefers the custom theme CSS to be stored with the theme files and not at an external repository.
In reply to Will Soward
Re: Moodle Mobile Custom CSS not working on Android devices
by Eric Phetteplace -
Thank you, I couldn't figure out why our custom CSS wasn't loading when it used to — we used to store it under local but I moved it to a directory under theme and now it works. Not sure if a Moodle or app update changed this behavior.