If you overwrite the language file, you will loose what you modified in it.
If you're doing a new translation or translating some new strings, you should make sure that you copy your translation before updating the translation file.
However, if you're just doing modifications to an existing translation file so that it suits your use case, you should do the modifications in the override area:
www.hikashop.com/download/languages.html#modify
When you do that in the override area, you don't loose your modifications when you update the translation file.