This is a known case with multi-dimensional products.
Generic variant product is dependent upon the Product as a partOf attribute. But in some scenarios when the GenericVariant product instance is modified without modifying the base product then sync deems that genericvariant instance as an orphaned one that should not be related to the product so it deletes the variant and recreates one.
Now in the checkout, the PK of the entry changes as the sync has created a new Online variant due to the above reason. Since the cart contains the entry of the earlier variant with another PK which could not be found, the error of "Object No Longer Valid" is thrown.
This is not traceable as the same product is available in the cart entry (but with a different PK)
The below approach of modifying the sync description through Backoffice-> System -> Multithreaded Synchronization should help to resolve this.
In the below screen, I have disabled sync of Product Variants [Variants] (The selected node). By default, it is ticked.

CX Jira References:
- https://cxjira.sap.com/browse/ECP-3394
- https://cxjira.sap.com/browse/ECP-5494