Mass Merging of Products with same SKU

Hi Guys,
Appreciate any help on this.
We’ve got 1000’s of products with the same SKU, as the same item fits multiple different motorcycle models which are listed individually. We current have our warehouse system pushing stock values into Veeqo via API and using a 2nd warehouse on Veeqo to import .csv’s to update supplier stock levels.
However what’s happening is just one variant takes all the stock for the SKUs, where as I need the stock quantity to update on all variants with the same SKU.
Veeqo support explained the manual method of merging products, but we’ve got thousands of SKUs that would need this. Can anyone think of a way to do this on mass ?