I'm not sure whether it's Excel doing this or not
Checking the csv file outside of excel (so in a text editor) will answer that for sure.
You should also check a product that was duplicated against the csv file to make 100% sure your editing process is not introducing variance to the product handle. If the handles don't match you might to do some digging to find out why.
Worth talking to support over, but do some of the checking above first, so you're armed with a bit more info.