Thank for the reply, Jason. I reopened the original CSV, and I copied and pasted the barcodes into Notepad, and they were still in scientific notation. I went back and changed the cell format from General to Number, and the numbers showed correctly in Notepad when I copied and pasted. Something must be going on in Excel when I resave the file after doing edits. I probably have to change the cell format before resaving.
With the duplicate problem, the handle was being used twice. The wholesaler that I get the data from adjusted the names of a lot of their products. When I did a product search in Shopify using the handle instead of the product name, two products with similar names came up most of the time, so I had to delete the one with the old name. I spent hours this weekend removing these more than once every time I tried to upload a correct CSV. The overwrite feature just didn't work on all of them. This why I don't trust it now because I can't see myself spending extra time trying to remove duplicates again.