This is a very special problem I met in Prestashop. I have a product, let's say a two color wooden stick, which is a normal 10" long stick. Half of it (5") can be blue and the other half red for example.
My product is this: Two color wooden stick. I have the following features: color 1 and and color 2 .
In the admin at the product's features I check red for the color 1 and blue for color 2.
Now the problem: when user filters using layered navigation, maybe they select blue for color 1 and red for color 2. This will result displaying 0 products as our wooden stick is inverse, but in the reality it's the same product.
How could I make that possible without duplicating the wooden stick product?
I see there is mismatching, your product 10" is not blue OR red, but blue-red in same time, so set two different colors is bad idea, instead I can propose you to do next, I hope when you said that you use color features it is named in Presta backoffice attributes, there is the difference between two this things in Presta, so:
in Catalog -> Product Attributes create new P.Attribute with name Color and for last option choose Color or textures in dropdown
add new Value for this new Color p.atrribute named e.g. "blue-red" and upload texture (img) that contains both colors. Repeat this procedure as much as needed.
in Layered navigation use this new p.attribute instead old
OR
another idea, create using same way 2 different color attributes Color1 and Color2, no textures, just use real separate colors there like "red", "blue". Then in product create combinations of this two colors and assign it to product.
In this case in layered navigation you will can set 2 filters - Color1, Color2 and customers will can to choose it. But, imho, first solution is better for UX.