I figured the Cloud was the reason for my save games being deleted so I went to properties -> updates and unchecked the tick box for the steam cloud.

Turns out it wasn't really the problem but the tick box that I unchecked to disable it is no longer there.
How do I turn it back on?

Valve disabled Steam Cloud for the time being because it was messing with people's save files. Once they fix it, you should be able to turn it back on.

Much appreciated, I figured I had messed it up. Thanks a bunch.