To fix a product which has stopped calculating. Go to the wp-dashboard > CPO-Options
And delete all the Attributes/options related to the products modules.
Go back to the product>CPO builder and go through the modules and save them(with DB turned on) one by one. This will recreate the Attribute/options in the database. Save the product and it should work.
When duplicating a product, the link to the attributes are instanced(a symbolic link to the option) be careful not to save these modules with DB on, in any duplicated product as you will change it from instanced to direct link, and overwrite/takeover from the original product(This renders your original product useless)
You can add new modules to the duplicated and save those to DB, as long as they have a unique name, as they will become new modules, linked directly to your duplicated product. I think if you need to change a module on the duplicated product which is instanced to the original product, you need to change the slug name to a unique name, before saving it with DB on. Remember, any visual changes or changes to labels etc(the ones without a yellow triangle) you do not need to tjek the save to DB option, and you can freely change these things without affecting the original products.
It takes a little disciplene to wrap your head around, but once you get it, it seams to make sense. I am sure the dev is working on ways to warn/avoid this issue.