Hi,
The Characteristic/Variants algorithm will change in the next HikaShop release.
There were some troubles when you edit a product and you remove a characteristic from a product.
For the moment I recommend you to delete the duplicate variants combinations and deactivate the option "auto variants" if you prefer to manage manually your variants and not let HikaShop populate it.
But with the next release you will be able to re-activate the feature, the algorithm will manage more cases (like a better support of the characteristic removal)
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.