Hi,
It's not possible that HikaShop delete orders and custom fields from the database during an update. There is no such code which could do that.
I'm guessing that during the update, some table structure couldn't be updated successfully and thus the MySQL queries loading the orders/fields crash and you don't see any on the listings, or something like that.
I would recommend to follow the procedure here:
www.hikashop.com/en/support/documentatio...lity-issues.html#SQL
If what I'm thinking is right, that should allow you to fix your issue.