Thanks for your project. I was able to reproduce your problem at first, but that was due to an unresolved maven problem. I have upgraded to m2e 1.0 in my workspace and the pom.xml was initially causing some errors.
The result was that maven was able to compile the project, but it could not be compiled inside of Eclipse. This further meant that even though class files were generated, there was no crosscutting model.
Because of this odd state, AJDT thought that everything was ok, but the crosscutting model was empty. So, it allowed you to do a push-in even though it didn't know where to push them in to (and so they were simply deleted).
Could this be the behavior that you see? Does your pom.xml have any error markers on it? Do you see AJ gutter markers in your AJ files?
If this is the case, then perhaps the solution is to be more explicit and warn users when this kind of error occurs.