Discount one option, not the whole product
Mark down one size or color. Same Product options block as Count Stock, Quantity, and Price.
You should not clone a product just to mark down one size. Option subsidy does that on the same SKU.
Open the product. In the Product options block — the same screen as Count Stock, Quantity, and Price — set the discount / subsidy on the value you want cheaper.
The catalog stays one product. Shoppers see a sane price on that size or color.
Questions about option subsidy
Product editor → Product options block. Same screen as Count Stock, Quantity, and Price.
No. The subsidy sits on one option of the same SKU.
Same block, different field. Count Stock is quantity. Subsidy is the markdown on that value.