Variables colors don't update

Hi there!
Not so long ago we switch our components in Design System from Color Styles to Variables Colors. However, after publishing changes and updating design files, I still can see Color Styles in our components instead of Variables in design files. I assume, It’s because of overrides made by previous designer, but there are way too much mismatches for a just overrides. 

First screenshot is from our Design System, where we switch to Variables, so it’s true
The second one is from Design File with Color Styles

Can you help please?
Thanks