Product variations dissappear causing orders to be empty

[Moderator note: Topic title de-capped. Please do not shout at us.]

Please help! We have a live website with thousands of customers unable to purchase! 🙁

I backed up! When I update Woocommerce (having made sure all other plugins are up to date) (Table Rate, Product Bundle, Smart Coupon) (all others off) I click run database updater, the entire site crashes, I narrowed that down to WPML (turned that off and removed from DB)

Now when I go back to backed up version to try again, the DB updater deletes ALL product variations, therefore the orders have no product info in them either! I also have an item now stuck in the cart, I cannot add or remove it.
I am using Flatsome theme but this is up to date and seems to be working as if I switch to another theme I still have the variations missing and the item in the cart.

I can see you’re busy so I thank you in advance!

https://wordpress.org/plugins/woocommerce/