You can also save to a Cloud storage service. I save my projects on Google Drive. This way, I am always protected from losing my projects when a hard drive fails. Also, make a second backup in case your working copy gets corrupted.
You can also work offline; however, to continue working, you need to log in every week (correct me when I am wrong).
I understand your concern, especially with long-term projects. I am sure Scirra backs up its servers regularly, so I think we are safe even when a server fails. If the whole team disappears from Earth (which is very unlikely), it depends on Scirra's precautions to guarantee their service.
The C3 project format is a zip file. You can check this by changing the extension of your project to .zip. Then, open that .zip file, and you will see all your files.
You can also take precautions in case a disaster strikes. Write important sections of your game in Javascript code (methods/functions). Store the game's resources on a cloud service, as mentioned above. Document your game in detail.
I think we are quite safe when following what I wrote above. However, I am not a Scirra employee, so I can be wrong. Only Scirra can answer your concerns, so maybe it is a good idea to contact their support team and ask. Scirra is easy to access and they respond mostly within 24 hours.
I hope this helps.
Bad_Wolf
(not so bad once you know him)