For the reason beyond my imagination Wordpress never had chance to get real theme updater (i.e. the one that would actually update only changed files) and instead offers a-joke-called-updater, that rips everything off from theme folder and unpacks everything from .zip with newer version.
This means, that I have to manually upload (via FTP) any changed / created translation files for all my themes, because every time theme is updated by weird Wordpress theme updater, it rips of contents of
languages folder and replaces it with contents of the same folder found in newer version of theme.
Is there any way to workaround this problem? Or the only option, I'm left with (except for what I am already doing -- i.e. manually updating translations over and over again) is to convince theme author to accept my translation and include it in next official release of his or her plugin?