Hi,
I'm sorry but I don't understand your issue.
HikaShop automatically generate thumbnails based on the sizes you configure in the HikaShop settings.
So if you want different sized thumbnails, just change the settings and HikaShop will generate the new thumbnails out of the original images you uploaded.
If you directly upload new images with the same names as old ones via FTP, the thumbnails won't be regenerated. You need to delete the thumbnails folders in the images/com_hikashop/upload folder and then HikaShop will regenerate the thumbnails for you.