That's a complicated one! You should contact the RG hhelp centre (icon bottom of any page). It will tell you how to delete one which is very simple. But saving both sets of stats and merging them is anyone's guess. So ask that question and you will probably get the offer of emailing RG. Do so!
I did the same thing. I had uploaded a paper and much later decided that it should be in a different category and uploaded it again. Then when I was going through the process of deleting the first upload I was warned that I would lose all the recommendations and reads, so I left things as they were. I don't think the duplication matters, and the increased visibility may even slightly increase the likelihood of somebody reading or downloading your paper. However, I've come to realize that RG scores don't have much significance anyway.