A simple solution is you keep the name of the new version application same as the old one.
Then just copy the same file in the folder which you have mapped as root folder.
Now when you paste the application, it will ask you to copy and replace or dont copy options, here choose copy and replace option.
This will replace the application but because the name is same all your qlikview settings will remain same.
The reason is all the information about the document CAL is stored in .Shared and .Meta file. and those files will have the same name.