Hello,
We improved the way that the email template are managed in HikaShop 3.0.1
You can see an asterisk ( * ) near "default" ; it means that you have an override for the "default" template.
And the philosophy behind override is that, they are kept during updates.
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.