Hi,
Depending the option "auto variant", HikaShop will try to generate the variants for the product using the characteristic values.
If you remove a characteristic, HikaShop is trying to delete the variants which are not useful (which are duplicates) but there are some cases when the algorithm is not working properly.
I am actually working on a new algorithm for the variant generation ; in order to prepare the integration of characteristics/variants of HikaMarket (which will become the new product edition system in the HikaShop backend too).
So in the next HikaShop release, this variant duplicate should be fixed.
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.