Don't worry, your translations are safe (unless the Zen Cart team are planning to start including Croatian translations with core Zen Cart :laugh:).
This is because all your language files named or located in places where the Zen Cart don't go. It's any changed you make to your template, such as in your stylesheet that are at risk. What you need to do is:
re-name any and all directories called "classic" to something else,
edit your classic/template_info to give your template a new name,
go to Admin > Tools > Template Selection and choose your new template and
go to Admin > Tools > Layout Box Controller and re-select your sideboxes.
Then you're bulletproof.
On your translation, I'm hoping that you will package it up and submit it to the downloads section. That would certainly keep it safe! Or if you wanted, you could zip up the files and send them to me and I would be happy to package it up for you.