Hi,
I actually just tried to reproduce:
I create a product, enter a name and a description and save.
Then, I edit the translation overrides for the name and description with the popups and save each popup and save the product.
I check the translation override files and they are all fine with the latest build.
I actually do think that your problem comes from not having the patch I was talking about in my previous message.
If your enter a translation override with HTML with double quotes (like it can happen if you add a link with the description editor for example), without the patch, you'll have an invalid translation file. Then, it you edit another translation or the same one and save it again, it won't be able to load the translation file and then it will save an empty translation file.
So the patch I talked about would avoid that unless someone would manually modify the translation override file incorrectly. Now, I've added another patch so that if the system can't load a translation override file because there is a mistake in it, it will leave it be and return an error.
You can download the HikaShop install package on our website and install it on yours so you'll get both patches and it should then work fine for you too.
Sorry for all the troubles you went through with the translation override system and thanks for the additional details on how to reproduce the issue.