Ok, the issue was when someone purchased inside the store, not the website. If the store owner puts quantity to zero on backend, hikashop deletes the item. However, it appears to not delete if the quantity is set to zero on the frontend.
EDIT: I had to put back the original file for the to work.... In components/com_hikashop/views/cart/view.html.php. There was an edit you had given me that was causing the delete issue in topic # 202494 (item#2).
So, we will continue to test and hopefully that issue doesn't return.
Thank for your time and effort, we appreciate it.