Hi,
If you did your customizations like we recommend (via the Display tab of the HikaShop configuration for CSS, and via the Display>Views menu for the views), you should not loose your changes when you update HikaShop.
Still I would recommend to do a backup before in case something goes wrong, you never know.
Regarding the display of out of stock products, you're looking at the global setting of the HikaShop configuration, but each products listing has its own option which can overrides the behavior of the display of out of stock products for the listing:
take.ms/YxywB
So it's totally possible that it is not a bug, but just that you have that option turned off in your products listing menus/modules and thus the out of stock products won't display in the listings even if the main configuration setting is turned off.