Hi,
The HikaShop update system has been made to update the files and keep the configuration and the overrides.
You have to be sure that you did not modify some HikaShop core files and you right used the override system (for the views and CSS).
We still recommend to make a backup before an update ; in case when something not good and you want to roll back.
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.