Other possible user errors with configuration of projects (at least for me) is selecting the wrong file format, e.g. Transit instead of DOCX. When CafeTran Espresso freezes or you assume that it freezes and kill the app, the PT will get destroyed too.
When you make an Error in project configuration the selected Project Template will get destroyed. That is: e.g. when you have set the project to a multi-file project and select a folder that contains one SDLPPX, this package won't be loaded (that's understandable). But when you restart CafeTran Espresso, the Dashboard will list the name of the PT, but not all assigned and selected resources will be listed.