This sounds like a business decision. Get your product people and your UX people involved.

If you don't have those, there are multiple things you could do.

1. Add a date of creation to your shopping carts. You can then experiment with either prioritizing the latest one, or asking the user to choose between their last two
2. Merge them into one. This is very likely not what the user wants, especially if their older cart is older than, say, 24 hours.
3. Speaking of which, shopping carts should expire. Most ecommerce platforms I've worked with usually archive the shopping carts after some time (15-60 mins). During this time they keep the items in the cart as reserved so no two people end up competing for the same stock.
4. Expired carts can be stored so you can send an email to your user with a link that allows them to get back to their unfinished purchase.

So with that in mind, consider the following questions:

• How relevant is each shopping cart to the user? Do you have a way of chosing the "most" relevant one?
• Are you dealing with physical goods where you need to keep track of the stock? Then you probably need to "reserve" the appropriate amount of items for each cart, and you'd need to "expire" each cart
• Do you ever want to present your users with a choice of two shopping carts? If yes, create an interface where they can do that. If no, consider prioritizing the latest cart and consider sending an email to the user reminding them about the earlier.

Your problem is with having too many options, not with having no choice, so you need to either get your peers involved, or start A/B testing. I think you'll only get subjective answers here.