Hi,
Deleted variants are deleted.
However, the system will display the choice in the characteristic dropdown if it is needed for another variant.
For example, if you have two characteristics: color (red and blue) and size (M and L).
If you remove the blue L variant, it will still be selectable in the dropdowns on the product page as L is necessary for the red L variant and blue is necessary for the blue M variants.
Now I don't know your specifics, so it might be something else.
In that case, please describe precisely the problem and how you setup your product/variants and provide a link to it.