No, your existing Chrome bookmarks stay where they are
Caves of Wonders (CoW) does not delete or change your existing Chrome bookmarks. Your bookmark folders remain in your browser.
Import creates a copy
When you use Import Bookmarks, CoW creates a copy of your existing Chrome bookmarks. The imported collection is placed in an Imported Cave, and your existing folders become Chests.
Learn how to import Chrome bookmarks without losing folders.