How to update product quantities based on SKU instead of title?

Hi ,
I have large number of products from my supplier
the problem is too many products have the same title but different SKU
they are all uploaded now to the store using third party app but I’m not using it anymore
now when I try to update quantity using shopify admin
I keep getting this error :

product were ignored because they already exist in your store for large number of product
I spoke with customer service but they weren’t able to solve the issue
for example I have :
product title SKU Quantity
Xbox 1001 5
Xbox 1002 10
when I make the update one of them only got updated
is there anyway to get over this ?
Kind Regards

Nothing !!