The Problem:
You've created an SSIS solution in Visual Studio. When opening the solution to edit a package, a few are missing from the Solution Explorer pane. Every time you try to 'Add Existing Package' or 'Copy & Paste' it creates a new instance of the package.
The Solution:
Instead of right-clicking and selecting 'Add Existing Package', right-click on the Solution itself and click 'Add > Existing Item' (Shift+Alt+A). Now you can CTRL-select all of the items missing from your Solution Explorer and click 'Add'.
The Wrong Way:
The Correct Way:
If you're interested in a little more about WHY this happens billinkc has a some good information here on StackOverflow http://stackoverflow.com/questions/15502567/ssis-package-not-visible-in-vs-2010