When I encountered this error it is because I wanted two different install locations for the same program. Specifically Program_A was published to two spots online and after changing a small thing in the program, I wanted them to both be installed on the same machine, but from different ClickOnce links.
So after receiving that error, instead of attempting to tweak the manifest I changed the options. Project Settings -> Publish -> Options -> I edited [Published Name, Suite name:, Product name:]. You may not have to change all three.
I now have both installs running. ClickOnce will install in a different directory, but it will remove the first desktop shortcut.
If you dont want to go that route, manifest information is here.
https://msdn.microsoft.com/en-us/library/ws1c2fch.aspx
And your manifest is usually is located under bin/debug(release)/yourprogramname.application.