How do I stop selling one size or colour without deleting the whole product?

Turn that variant off instead of deleting it.

1. Open the product and scroll to the Variants card.
2. Find the row, for example "XL / Red".
3. Untick its Active checkbox.
4. Click Save.

Shoppers can no longer buy that combination; if they pick it, it shows as out of stock. All other variants stay on sale. The row keeps its price and stock, so you can tick Active again later to bring it back.

If a variant is only temporarily sold out, you can instead set its Qty to 0 until it is back.