It seems as you have clicked on Open file instead of Save as.
With open file it tries to open the file directly and if it can't do that you get such a message. Just upload the file and when downloading be sure to select save as. Also, if you want to download to test it, don't download it to the same place where the uploaded file is also located. Otherwise you get duplicates.
Make a new map somewhere, other partition or disk is recommend, and use that one for testing purposes.