Hi,
The override area you see when you edit a language file under the Languages tab of the HikaShop configuration is the general override file of Joomla. It contains all translation overrides, made via HikaShop or via Joomla's interface.
So, if you made a translation override via the Joomla translation overrides interface, it's normal you see it in the override area of HikaShop.
HikaShop is not interfering with that.
The first thing to do is to activate the language debug setting of the Joomla configuration. That way, you'll see if there is an error in the override file (which could prevent Joomla from taking into account some or all the overrides in there).
docs.joomla.org/Special:MyLanguage/Debugging_a_translation