Right. The Language customization tool does not support empty strings at the moment, I am afraid. You could try and use the following hack: instead of the empty string, use the following as your local customization:
It is just an empty span HTML tag that should do nothing when printed at the screen but the tool could consider it as a valid customization. Just be aware that this is applicable only for strings that are displayed as standard HTML texts in the user interface. There are strings used as email subjects, for example, where thick trick can't be used.