If you are only playing with one character and you upload that data, it will be on the back up server in case you need to download that data again from a lost device, or you move devices, etc.
If you then create a new character, play that character on your account, then upload that new character. It will REPLACE the data you already have on the server.
At that time, the only data on the server will be what you have uploaded most recently. In your case that second characters data will be stored over the original data and that original data will be lost.