It is still unclear what the issue was, and you should make sure to clear your preferences after a crash.
However, being that this is no "save" command, there are two things that you CAN do:
a) Make a snapshot. This saves an exact copy of your project in the browser. The standard shortcut is Command-Shift-D.
The snapshot will be named including a timestamp. I think this is the best way to get peace of mind, also if something in your editing goes wrong you can easily pick it up at that point in time.
EDIT: you can even assign it the standard Command-S shortcut, if you like.
b) Export XML. This is a text-based description of your project, which you can save anywhere you like, even e-mail or whatever you need to do with it. Select the project, and do File->Export XML...