I'd have thought you needed to base your new file on the second file with the current SKU list in case any are added or removed or the UPC is changed.

So, I'd copy file 2, making it file 3 (for upload) and add a VLOOKUP formula to get the price from file 1.

Alternatively, just copy file 1 and make it file 3. Then replace the existing quantity values with a VLOOKUP to get the new quantity field from file 2.

I think either approach could work but I don't know enough about your processes to be definitive.

Regards, TMS