How do you know that, when you save a project, it is saved correctly? Sure, you should save the project you are working on constantly incase your computer decides to crash. But what if, everytime you are saving your project, it is not being saved correctly. I have been working on a track using Battery3. Saved the project constantly, like I always do. Reloaded the project today, only to find that the last 13 backups I made of the project all incorrectly saved the Battery3 settings. All the changes I had made to Battery3 within those last 13 project backups were lost with Battery3 being loaded with the same default settings in each of those 13 projects.
The only thing I can think of is to, in the future, save Battery3’s settings using it’s own “Save Kit” option. Never had this problem before with Battery3 and have been using it for over 2 years. Very frustrating!!! 
The problem with cases like this are that they seem so random - I was doing nothing out of the ordinary. There doesn’t seem to be any reason for Cubase to suddenly decide to not save my Battery3 settings within my project. But there must be some logical reason - computers are logical - they aren’t random!!
If it has happened this time then what’s to say the same thing won’t happen again, perhaps with a different VSTi, on a project that I consider to be far more important!! All I can do is carry on doing what I am doing, constantly backing up my projects as I am working on them. But, if I am backing up projects that will not load up correctly, that kind of defeats the point of doing the project, let alone backing it up!