Hello,
We Really Apologize about the Inconveniences caused!
Both the Files can be used to change Colors. If you use the css/colors.css File, you will need to change all the Color HEX Codes manually in the File. But if you use the css/colors.php File, you can simply use it as css/colors.php?color=HEX (without #) which will change all the HEX in the File automatically making it convenient.
Hope this Helps!
If you are still facing an issue, it would be great if you can please provide us with a Live URL so that we can check out the exact issue and provide you with a more accurate solution for this. Thanks for your Patience.
Meanwhile, do let us know if we can help you with anything else or if you find any further issues with Canvas.