I don't have the Big Fish Games version of VV3 to test with, but I haven't yet been able to reproduce anything like this in my testing. I will let you know if we are able to figure out why you are losing your games.

In the meantime, one thing that would help you recover more easily if that happens to you again is to make backups of your savegame files periodically. If you have a backup, you can recover your game to the last point at which you made a backup. You can find the procedures for VV3 here.