Steam cloud saves often cause conflicts with the world saved on your computer, it is just not a reliable process unfortunately :( they can easily get de-synced. Which can cause the world save on your computer to get messed up if the old cloud save takes priority.

I would turn it off for VH if I were you so that you can be confident the world save on your computer is the controller for your progress. I'm sorry for your lost efforts :(

Edit: It's a good idea to turn off the Steam save for most games tbh. Especially games like this where you're putting a lot of time into creating custom bases.