What I do when I want to make changes to an app that I have already downloaded and published is, go back into developer and make changes. I then re-download and publish to my server replacing all files of the working app with the new ones.
If it is a small change I sometimes make the changes to the app in developer then re-download and copy over the changes into specific files in the published app. (this is very dangerous if you don't know what you are doing)