Yeh, I sent an email to support@c9.io and the guys there sorted it out for me eventually after restoring a few backups. As we didn’t know exactly when the problem had happened they had to go back through the backups, restoring them until my stuff reappeared. Luckily it was there on the earliest backup that they had, which was only from about two weeks before I reported the problem.
Sorry to hear that it has happened again - they said they didn’t know why it had happened last time but my stuff appears to be OK this time.
As recommended by them, I push my stuff to a git repository regularly now, just in case.
Hope they manage to sort it for you.