I’ve found a solution a few minutes after posting this question.
In case anyone is also looking for that:
1. create wp-content/languages/plugins/ directory
2. copy selected ACF translation file (.po and .mo) from ACF plugin lang/ folder to created wp-content/languages/plugins/
3. customize the translation with e.g. Poedit or any other program for editing .po files and then generate .mo
This way your translation will be preserved even after plugin update.
Welcome to the Advanced Custom Fields community forum.
Browse through ideas, snippets of code, questions and answers between fellow ACF users