Hi,
HikaShop stores your images in the folder images/com_hikashop/upload (or media/com_hikashop/upload for old versions).
That's where you have your original images. You need to make sure these are valid (via FTP for example, or the media manager of Joomla).
Then, when HikaShop has to generate thumbnails, it will generate them with the same name in the thumbnails sub folders of that folder.
When you change the size settings of your thumbnails, a new subfolder of the thumbnails folder is created with new thumbnails generated for that specific size.
So if you have different size of thumbnails, and if you change the images settings, new thumbnails folders keep being created when the thumbnails of the specified sizes are necessary.
If you want to clean them, simply delete the whole thumbnails folder. HikaShop will recreate the folders with the thumbnails when needed. So if you had old corrupt thumbnails of your images, deleting the old thumbnails will allow HikaShop to regenerate them with the new correct origin image.