If you have one cell for SKU and one cell for Barcode then it shouldn't be a problem as long as they're not using the same VLOOKUP code (obviously the index number criteria for the formulas would be different due to positioning). I don't understand what your problem is. If there's no matching SKU for a product then it shouldn't come up with anything and then the user will have to use a barcode search.
I'm not sure if this is what you're looking for but I gave it a shot.
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