No. A HomeRunner Toolkit update does not replace translations you have already made on your site.
Starting with Toolkit 3.288.0, the Search Bar Pro module includes built-in Dutch and German for its guest-facing labels, and the Core Translations module includes built-in Dutch and French for the booking widget and calendar labels. The built-in wording is used only for labels that have no translation of their own on your site. Any label you translated in WPML String Translation, Loco Translate, or a language pack keeps your wording after the update.
If some labels still show English. Translate those labels in WPML or Loco Translate as before. The built-in set only fills the gaps.