Are you using Dropbox?
I’ve the feeling that sometimes Dropbox can corrupt the project file …it doesn’t always happen, only like 1 out of 60 times…
Also it doesn’t corrupt the project file completely, just parts of it… sometimes I had projects that opened but missing half of the tracks. Sometimes projects that didn’t want to open at all, etc…
Now, when I’m doing my last save of the current project, I always save 3 times with 3 different names ( like v10, v11, v12 ) and I leave the time to dropbox to fully synchronize the project file, BEFORE closing the project and quitting project.
I’ve the feeling if you save then directly close and quit Cubase, it can messes up things.