Hi,
The refresh system on your characteristic dropdowns is a custom development that you have added. By default, HikaShop display all the possible values in all the dropdowns.
Unfortunately, I don't know how your custom code works so hard to say if it's because of that, or because of something else.
One thing you can check is that if you go in the "manage variants" button of your new product, you get the variants that you need. If not, then it would explain the issue and you would have to use the "new" button there to create the missing variants.
If yes, then all I can think of is that the problem comes from the customization of the code that was made.