Visual Studio 2012 Business Intelligence SSIS packages missing

The authoritative source of what's in a project is going to be the ProjectName.dtproj file.

Inside of that will be entries for the packages that comprise the project. For a non-package deployment model, it's trivial to edit the file by hand and make your stuff show up.

It's way too much effort to do that by hand for a 2012+ project deployment model. Open the Project in Visual Studio (ssdt/bids) and right click on the project. Click Add Existing Item (not add package) and then click the "missing" package. Check your .dtproj file in and all is right with the world.