Good variant rows
Handle,Option1 Name,Option1 Value,Option2 Name,Option2 Value
linen-shirt,Size,Small,Color,Navy
linen-shirt,Size,Medium,Color,Navy Duplicate option combination example
linen-shirt,Size,Small,Color,Navy
linen-shirt,Size,Small,Color,Navy Inconsistent option names example
linen-shirt,Size,Small,Color,Navy
linen-shirt,Shirt Size,Medium,Color,Navy Blank option value example
linen-shirt,Size,,Color,Navy Why repeated handles are not the problem
Repeated handles are how Shopify groups variants under one product. Your variants are not haunted. Probably. The problem is conflicting option structure inside the group.